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b/preprocessing_scr/CNA.ipynb |
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{ |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": 1, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"from __future__ import print_function\n", |
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"import pandas as pd\n", |
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"import os,sys\n", |
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"import pybedtools as pbt\n", |
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"from StringIO import StringIO\n", |
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"import numpy as np\n", |
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"import matplotlib.pyplot as plt\n", |
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"import numpy as np\n", |
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"import time\n", |
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"from mapper import expand, parse_mapping_table, apply_mappers\n", |
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"%matplotlib inline\n", |
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"\n", |
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"\n", |
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"chr_dict = dict(zip(range(1,22),map(str,range(1,22))))\n", |
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"chr_dict.update({22: 'X', 23: \"Y\"})\n", |
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"\n", |
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"root_dir = \"/home/olya/SFU/Hossein/v2/\"\n", |
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"gene_coords_file = root_dir + \"ref_GRCh37.p5_top_level.gff3.bed\" # must contain chromosome, start, end and Entrez Gene ID for hg19" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"# TCGA \n", |
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"\n", |
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"Assume that segmentation files from GDAC : http://gdac.broadinstitute.org/runs/stddata__2015_08_21/data/*/*snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt are dowmnoaded\n", |
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"\n", |
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"1) Filtering segments:\n", |
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" - segments containing less than 5 probes removed\n", |
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" - keep only segments with segment mean below -0.23 or above 0.2. This means that one copy gains and losses are detectable when their CCF (canncer cell fraction) is 0.3 or higher. \n", |
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" \n", |
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"TODO: remove segements overlapping with germline CNA forund in normals (add this as the first step)\n", |
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"2). For each samples aggregte to gene-level:\n", |
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" - rename chromosomes 22 and 23 to X and Y\n", |
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" - overpal segemntation file with Entrez gene coordinates for hg19\n", |
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" - if a gene overlaps by multiple segments, keep the one with most extreme values" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 2, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"num_marker_thr = 5\n", |
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"# to detect 1 copy gains or losses presenting at CCF >= 0.3\n", |
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"pos_seg_mean_thr = 0.20\n", |
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"neg_seg_mean_thr = -0.23 \n", |
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"\n", |
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"preprocessed_dir = root_dir+\"preprocessed/CNA/\"\n" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 19, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"### functions for TCGA and CCLE #################################\n", |
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"def filter_lowconf_segments(df,num_marker_thr,pos_seg_mean_thr, neg_seg_mean_thr ):\n", |
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" # filter low-confidence segments with too few probes\n", |
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" df = df[df[\"Num_Probes\"] >= num_marker_thr ]\n", |
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" # filter low-confidence segments with Segment_Mean too close to zero:\n", |
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" df = df[ (df[\"Segment_Mean\"] >= pos_seg_mean_thr) | (df[\"Segment_Mean\"] <= neg_seg_mean_thr)]\n", |
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" return df\n", |
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"\n", |
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"def sample_type(barcode):\n", |
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" if barcode[13:16] in [\"10A\",\"10B\",\"11A\",\"11B\",\"10C\",\"11C\"]:\n", |
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" return \"Normal\"\n", |
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" else:\n", |
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" return \"Tumor\"\n", |
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"\n", |
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"def find_matching_normal(tumor_barcode,barcodes_list):\n", |
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" patient_id = tumor_barcode[:12]\n", |
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" normal_barcodes = []\n", |
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" for barcode in barcodes_list:\n", |
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" if barcode.startswith(patient_id) and sample_type(barcode) == \"Normal\":\n", |
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" normal_barcodes.append(barcode)\n", |
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" return normal_barcodes\n", |
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"\n", |
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"def cnv2bed(seg):\n", |
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" #cnv_bed = seg[[\"Chromosome\",\"Start\",\"End\",\"Segment_Mean\"]]\n", |
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" #cnv_bed.columns = [\"chrom\",\"start\",\"stop\",\"Segment_Mean\"]\n", |
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" cnv_bed = seg.rename({\"Chromosome\":\"chrom\",\"Start\":\"start\",\n", |
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" \"End\":\"stop\"},axis=\"columns\")\n", |
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" cnv_bed = cnv_bed.loc[:,[\"chrom\",\"start\",\"stop\",\"Segment_Mean\",\"Sample\",\"Num_Probes\"]]\n", |
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" return pbt.BedTool.from_dataframe(cnv_bed)\n", |
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"\n", |
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"def bed2cnv(cnv_bed):\n", |
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" cnv_bed = str(cnv_bed)\n", |
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" if len(cnv_bed) > 0:\n", |
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" seg = pd.read_csv(StringIO(cnv_bed),sep = \"\\t\",header=None)\n", |
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" seg.columns = [\"Chromosome\",\"Start\",\"End\",\"Segment_Mean\",\"Sample\",\"Num_Probes\"]\n", |
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" seg = seg.loc[:,[\"Sample\",\"Chromosome\",\"Start\",\"End\",\"Num_Probes\",\"Segment_Mean\"]]\n", |
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" else:\n", |
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" seg = pd.DataFrame(columns=[\"Sample\",\"Chromosome\",\"Start\",\"End\",\"Num_Probes\",\"Segment_Mean\"])\n", |
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" return seg\n", |
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"def remove_ovelapping_segments(tumor, normal,sample_name):\n", |
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" tumor_bed = cnv2bed(tumor)\n", |
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" normal_bed = cnv2bed(normal)\n", |
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" tumor_wo_germline = tumor_bed.subtract(normal_bed,r=True,f=0.8,A=True)\n", |
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" tumor_wo_germline = bed2cnv(tumor_wo_germline)\n", |
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" n_segs_removed = tumor.shape[0] - tumor_wo_germline.shape[0]\n", |
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" if n_segs_removed*1.0/tumor.shape[0] > 0.5 and n_segs_removed>5 :\n", |
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" print(n_segs_removed,\"of\",tumor.shape[0],\"segments removed in\",sample_name,\"due to overlap with normal\",file = sys.stderr)\n", |
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" return tumor_wo_germline\n", |
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"\n", |
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"def cnv2genelevel(cnv_bed,gene_intervals_bed,sample_name,verbose = True,sorted_index = \"\"):\n", |
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" \n", |
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" # intersect \n", |
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" cnv2gene = str(gene_intervals_bed.intersect(cnv_bed,wb = True,wa=True))\n", |
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" if len(cnv2gene)==0: # if no intersection, return all zeroes\n", |
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" print(sample_name,\"has no genes with altered CN\",file = sys.stderr)\n", |
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" return pd.DataFrame(columns=[sample])\n", |
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" cnv2gene = pd.read_csv(StringIO(cnv2gene),sep = \"\\t\",header=None)\n", |
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" cnv2gene = cnv2gene[[3,7]].copy()\n", |
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" cnv2gene.columns = [\"gene\",\"Segment_Mean\"] \n", |
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" \n", |
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" # find genes overlapping with more than one segment:\n", |
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" # take the most exterme segement_mean value\n", |
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" \n", |
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" dups = cnv2gene.loc[cnv2gene.duplicated(subset=[\"gene\"],keep=False),]\n", |
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" if dups.shape[0] > 0:\n", |
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" cnv2gene = cnv2gene.drop_duplicates(subset=[\"gene\"],keep=False)\n", |
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" dups[\"abs_seg_mean\"] = abs(dups[\"Segment_Mean\"])\n", |
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" if verbose:\n", |
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" print(sample_name,\"contain \",len(set(dups[\"gene\"].values)),\"genes overalpped with more than one segment\",file=sys.stderr)\n", |
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" #print(dups.head(10),file=sys.stderr)\n", |
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" dups = dups.groupby(['gene'], group_keys=False).apply(lambda row: row.loc[row['abs_seg_mean'].idxmax()])\n", |
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" cnv2gene = pd.concat([cnv2gene,dups],sort=False)\n", |
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"\n", |
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" cnv2gene = cnv2gene[[\"gene\",\"Segment_Mean\"]]\n", |
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" cnv2gene.set_index(\"gene\",inplace=True,drop=True)\n", |
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" cnv2gene.rename(int,axis=0,inplace=True)\n", |
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" # add copy-neutral genes with 0s\n", |
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" \n", |
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" cnv2gene = cnv2gene.loc[sorted_index,:]\n", |
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" cnv2gene.columns = [sample_name]\n", |
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" return cnv2gene\n", |
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"\n", |
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"\n", |
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"### functions for GDSC and PDX #################################\n", |
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"\n", |
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"def CN2log2R(col, median_ploidy=2 ):\n", |
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" # this is fr GDSC only\n", |
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" lRs = []\n", |
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" genes = col.index.values\n", |
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" for code in col.values:\n", |
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" if not code == \"-1,-1,-,-\":\n", |
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" [max_cn,min_cn,zygosity,disruption] = code.split(\",\")\n", |
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" if int(max_cn) == 0:\n", |
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" lRs.append(-4.32) # CN=0 with 95% purity\n", |
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" else:\n", |
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" max_lR = np.log2(float(max_cn)/median_ploidy)\n", |
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" if not disruption == \"D\":\n", |
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" lRs.append(max_lR)\n", |
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" else:\n", |
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" if int(min_cn) == 0:\n", |
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" min_lR = -4.32\n", |
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" else:\n", |
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" min_lR = np.log2(float(min_cn)/median_ploidy)\n", |
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" if abs(min_lR) > abs(max_lR):\n", |
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" lRs.append(min_lR)\n", |
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" else:\n", |
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" lRs.append(max_lR)\n", |
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" \n", |
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" else:\n", |
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" lRs.append(np.NaN)\n", |
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" return pd.Series(dict(zip(genes, lRs)))\n", |
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"\n", |
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"def define_avg_ploidy(col):\n", |
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" n,pl = 0,0\n", |
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" CN_non_disrupted = []\n", |
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" for code in col.values:\n", |
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" if not code == \"-1,-1,-,-\":\n", |
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" [max_cn,min_cn,zygosity,disruption] = code.split(\",\")\n", |
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" n+=1\n", |
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" cn = (int(max_cn)+int(min_cn))*0.5\n", |
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" pl += cn\n", |
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" if not disruption == \"D\":\n", |
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" CN_non_disrupted.append((cn))\n", |
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" return pd.Series({\"avg_pl\":pl/n , \"median_pl\":np.median(CN_non_disrupted)})\n", |
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"\n", |
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"def clean_logR(logR_value, pos_seg_mean_thr, neg_seg_mean_thr):\n", |
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" if logR_value >= pos_seg_mean_thr:\n", |
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" return logR_value \n", |
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" elif logR_value <= neg_seg_mean_thr:\n", |
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" return logR_value \n", |
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" else:\n", |
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" return 0\n", |
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" \n", |
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"def handle_dups(df,corr_thr = 0.75):\n", |
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" '''Detect dupliated row IDs. Merge 2 or more rows with the same ID, \n", |
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" if averaged correlation in all pairvise comparision is >= corr_thhr;\\n\n", |
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" otherwise drop all duplicates. Keeps abs. max value (negative preferred).'''\n", |
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" dups = df.index\n", |
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" dups = list(set(dups[dups.duplicated()]))\n", |
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" if len(dups)==0:\n", |
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" print(\"No duplicated row IDs. Do nothing.\")\n", |
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" return df\n", |
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" print(len(dups), \"duplicated IDs in\",df.loc[dups,:].shape[0],\"rows found.\")\n", |
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" dups_merge = [] # if corr > corr_thr\n", |
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" dups_remove = [] # corr < \n", |
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" for dup in dups:\n", |
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" r = df.loc[dup,:].T.corr()\n", |
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" n_dups = df.loc[dup,:].shape[0]\n", |
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" r_avg = []\n", |
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" for i in range(0,n_dups):\n", |
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" for j in range(i+1,n_dups):\n", |
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" r_avg.append(r.iloc[i,j])\n", |
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" if np.average(r_avg) < corr_thr :\n", |
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" #print(dup,r_avg, n_dups)\n", |
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" dups_remove.append(dup)\n", |
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" else:\n", |
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" dups_merge.append(dup)\n", |
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" \n", |
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" # remove not similar duplicates\n", |
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" df_size = df.shape[0]\n", |
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" df = df.loc[~df.index.isin(dups_remove),:]\n", |
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" print(\"duplicate rows removed due to low correlation of duplicated profiles\",df_size -df.shape[0] )\n", |
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" df_size = df.shape[0]\n", |
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" \n", |
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" # merge simialr duplicates\n", |
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" d1 = df.loc[~df.index.isin(dups_merge),:]\n", |
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" d2 = df.loc[dups_merge,:]\n", |
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" d2 = d2.groupby(d2.index).agg(lambda x: -max(-x.max(),-x.min(),key= abs))\n", |
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" df = pd.concat([d1,d2])\n", |
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" df.sort_index(inplace=True)\n", |
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" print(\"Merged \",df_size-df.shape[0]+len(dups_merge),\"duplicated rows into\",len(dups_merge),\"rows\")\n", |
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" return df" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"### next few tabs demonstrate necessity of removing low-confidence and germline segments: \n", |
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"\n", |
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"(e.g. fragment 11:126596926-127130276 presents in both tumor and normal\n", |
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"therefore, it is germline; see chr11:126596926-12713027 in UCSC browser - it covers part of KIRELL3)\n" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 8, |
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"metadata": { |
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"scrolled": false |
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}, |
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"outputs": [ |
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{ |
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"name": "stdout", |
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"output_type": "stream", |
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"text": [ |
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"segemtns in tumor 204 segemtns in normal 121\n" |
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] |
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}, |
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{ |
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"data": { |
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"text/html": [ |
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"<div>\n", |
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"<style scoped>\n", |
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" .dataframe tbody tr th:only-of-type {\n", |
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" vertical-align: middle;\n", |
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" }\n", |
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"\n", |
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" .dataframe tbody tr th {\n", |
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" vertical-align: top;\n", |
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" }\n", |
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"\n", |
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" .dataframe thead th {\n", |
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" text-align: right;\n", |
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" }\n", |
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"</style>\n", |
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"<table border=\"1\" class=\"dataframe\">\n", |
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" <thead>\n", |
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" <tr style=\"text-align: right;\">\n", |
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" <th></th>\n", |
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" <th>Sample</th>\n", |
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" <th>Chromosome</th>\n", |
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" <th>Start</th>\n", |
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" <th>End</th>\n", |
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" <th>Num_Probes</th>\n", |
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" <th>Segment_Mean</th>\n", |
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" </tr>\n", |
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" </thead>\n", |
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" <tbody>\n", |
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" <tr>\n", |
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" <th>57803</th>\n", |
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" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
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" <td>11</td>\n", |
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" <td>456120</td>\n", |
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" <td>8896255</td>\n", |
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" <td>4489.0</td>\n", |
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" <td>-0.0113</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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306 |
" <th>57804</th>\n", |
|
|
307 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
308 |
" <td>11</td>\n", |
|
|
309 |
" <td>8899400</td>\n", |
|
|
310 |
" <td>8899668</td>\n", |
|
|
311 |
" <td>3.0</td>\n", |
|
|
312 |
" <td>-1.3344</td>\n", |
|
|
313 |
" </tr>\n", |
|
|
314 |
" <tr>\n", |
|
|
315 |
" <th>57805</th>\n", |
|
|
316 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
317 |
" <td>11</td>\n", |
|
|
318 |
" <td>8900394</td>\n", |
|
|
319 |
" <td>126596817</td>\n", |
|
|
320 |
" <td>67487.0</td>\n", |
|
|
321 |
" <td>0.0010</td>\n", |
|
|
322 |
" </tr>\n", |
|
|
323 |
" <tr>\n", |
|
|
324 |
" <th>57806</th>\n", |
|
|
325 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
326 |
" <td>11</td>\n", |
|
|
327 |
" <td>126596926</td>\n", |
|
|
328 |
" <td>127130276</td>\n", |
|
|
329 |
" <td>453.0</td>\n", |
|
|
330 |
" <td>-1.0306</td>\n", |
|
|
331 |
" </tr>\n", |
|
|
332 |
" <tr>\n", |
|
|
333 |
" <th>57807</th>\n", |
|
|
334 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
335 |
" <td>11</td>\n", |
|
|
336 |
" <td>127132920</td>\n", |
|
|
337 |
" <td>128342803</td>\n", |
|
|
338 |
" <td>864.0</td>\n", |
|
|
339 |
" <td>-0.0031</td>\n", |
|
|
340 |
" </tr>\n", |
|
|
341 |
" <tr>\n", |
|
|
342 |
" <th>57808</th>\n", |
|
|
343 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
344 |
" <td>11</td>\n", |
|
|
345 |
" <td>128342819</td>\n", |
|
|
346 |
" <td>128350888</td>\n", |
|
|
347 |
" <td>44.0</td>\n", |
|
|
348 |
" <td>0.2824</td>\n", |
|
|
349 |
" </tr>\n", |
|
|
350 |
" <tr>\n", |
|
|
351 |
" <th>57809</th>\n", |
|
|
352 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
353 |
" <td>11</td>\n", |
|
|
354 |
" <td>128353007</td>\n", |
|
|
355 |
" <td>134142530</td>\n", |
|
|
356 |
" <td>3708.0</td>\n", |
|
|
357 |
" <td>0.0082</td>\n", |
|
|
358 |
" </tr>\n", |
|
|
359 |
" </tbody>\n", |
|
|
360 |
"</table>\n", |
|
|
361 |
"</div>" |
|
|
362 |
], |
|
|
363 |
"text/plain": [ |
|
|
364 |
" Sample Chromosome Start End \\\n", |
|
|
365 |
"57803 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 456120 8896255 \n", |
|
|
366 |
"57804 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 8899400 8899668 \n", |
|
|
367 |
"57805 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 8900394 126596817 \n", |
|
|
368 |
"57806 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 126596926 127130276 \n", |
|
|
369 |
"57807 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 127132920 128342803 \n", |
|
|
370 |
"57808 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 128342819 128350888 \n", |
|
|
371 |
"57809 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 128353007 134142530 \n", |
|
|
372 |
"\n", |
|
|
373 |
" Num_Probes Segment_Mean \n", |
|
|
374 |
"57803 4489.0 -0.0113 \n", |
|
|
375 |
"57804 3.0 -1.3344 \n", |
|
|
376 |
"57805 67487.0 0.0010 \n", |
|
|
377 |
"57806 453.0 -1.0306 \n", |
|
|
378 |
"57807 864.0 -0.0031 \n", |
|
|
379 |
"57808 44.0 0.2824 \n", |
|
|
380 |
"57809 3708.0 0.0082 " |
|
|
381 |
] |
|
|
382 |
}, |
|
|
383 |
"execution_count": 8, |
|
|
384 |
"metadata": {}, |
|
|
385 |
"output_type": "execute_result" |
|
|
386 |
} |
|
|
387 |
], |
|
|
388 |
"source": [ |
|
|
389 |
"#file_path = \"../../TCGA/CNA/data/gdac.broadinstitute.org_CESC.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3.2015082100.0.0/CESC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt\"\n", |
|
|
390 |
"file_path = \"../../TCGA/CNA/data__2016_01_28/gdac.broadinstitute.org_CESC.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3.2016012800.0.0/CESC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt\"\n", |
|
|
391 |
"df = pd.read_csv(file_path, sep = \"\\t\")\n", |
|
|
392 |
"tumor_barcode = \"TCGA-ZJ-AAXJ-01A-11D-A42N-01\"\n", |
|
|
393 |
"t = df.loc[df[\"Sample\"]==tumor_barcode,:]\n", |
|
|
394 |
"t_shape = t.shape[0]\n", |
|
|
395 |
"n = find_matching_normal(tumor_barcode,list(set(df[\"Sample\"].values)))\n", |
|
|
396 |
"n = df.loc[df[\"Sample\"]==n[0],:]\n", |
|
|
397 |
"print(\"segemtns in tumor\",t.shape[0],\"segemtns in normal\",n.shape[0])\n", |
|
|
398 |
"\n", |
|
|
399 |
"n.loc[n['Chromosome']==11,:]" |
|
|
400 |
] |
|
|
401 |
}, |
|
|
402 |
{ |
|
|
403 |
"cell_type": "code", |
|
|
404 |
"execution_count": 9, |
|
|
405 |
"metadata": {}, |
|
|
406 |
"outputs": [ |
|
|
407 |
{ |
|
|
408 |
"data": { |
|
|
409 |
"text/html": [ |
|
|
410 |
"<div>\n", |
|
|
411 |
"<style scoped>\n", |
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" .dataframe tbody tr th:only-of-type {\n", |
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413 |
" vertical-align: middle;\n", |
|
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414 |
" }\n", |
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|
415 |
"\n", |
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|
416 |
" .dataframe tbody tr th {\n", |
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417 |
" vertical-align: top;\n", |
|
|
418 |
" }\n", |
|
|
419 |
"\n", |
|
|
420 |
" .dataframe thead th {\n", |
|
|
421 |
" text-align: right;\n", |
|
|
422 |
" }\n", |
|
|
423 |
"</style>\n", |
|
|
424 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
425 |
" <thead>\n", |
|
|
426 |
" <tr style=\"text-align: right;\">\n", |
|
|
427 |
" <th></th>\n", |
|
|
428 |
" <th>Sample</th>\n", |
|
|
429 |
" <th>Chromosome</th>\n", |
|
|
430 |
" <th>Start</th>\n", |
|
|
431 |
" <th>End</th>\n", |
|
|
432 |
" <th>Num_Probes</th>\n", |
|
|
433 |
" <th>Segment_Mean</th>\n", |
|
|
434 |
" </tr>\n", |
|
|
435 |
" </thead>\n", |
|
|
436 |
" <tbody>\n", |
|
|
437 |
" <tr>\n", |
|
|
438 |
" <th>57960</th>\n", |
|
|
439 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
440 |
" <td>11</td>\n", |
|
|
441 |
" <td>456120</td>\n", |
|
|
442 |
" <td>64200041</td>\n", |
|
|
443 |
" <td>34710.0</td>\n", |
|
|
444 |
" <td>0.0054</td>\n", |
|
|
445 |
" </tr>\n", |
|
|
446 |
" <tr>\n", |
|
|
447 |
" <th>57961</th>\n", |
|
|
448 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
449 |
" <td>11</td>\n", |
|
|
450 |
" <td>64208988</td>\n", |
|
|
451 |
" <td>64319750</td>\n", |
|
|
452 |
" <td>61.0</td>\n", |
|
|
453 |
" <td>-0.6748</td>\n", |
|
|
454 |
" </tr>\n", |
|
|
455 |
" <tr>\n", |
|
|
456 |
" <th>57962</th>\n", |
|
|
457 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
458 |
" <td>11</td>\n", |
|
|
459 |
" <td>64325209</td>\n", |
|
|
460 |
" <td>126596817</td>\n", |
|
|
461 |
" <td>37207.0</td>\n", |
|
|
462 |
" <td>0.0571</td>\n", |
|
|
463 |
" </tr>\n", |
|
|
464 |
" <tr>\n", |
|
|
465 |
" <th>57963</th>\n", |
|
|
466 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
467 |
" <td>11</td>\n", |
|
|
468 |
" <td>126596926</td>\n", |
|
|
469 |
" <td>127130276</td>\n", |
|
|
470 |
" <td>454.0</td>\n", |
|
|
471 |
" <td>-1.0760</td>\n", |
|
|
472 |
" </tr>\n", |
|
|
473 |
" <tr>\n", |
|
|
474 |
" <th>57964</th>\n", |
|
|
475 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
476 |
" <td>11</td>\n", |
|
|
477 |
" <td>127132920</td>\n", |
|
|
478 |
" <td>132080656</td>\n", |
|
|
479 |
" <td>3591.0</td>\n", |
|
|
480 |
" <td>0.0449</td>\n", |
|
|
481 |
" </tr>\n", |
|
|
482 |
" <tr>\n", |
|
|
483 |
" <th>57965</th>\n", |
|
|
484 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
485 |
" <td>11</td>\n", |
|
|
486 |
" <td>132080885</td>\n", |
|
|
487 |
" <td>132099465</td>\n", |
|
|
488 |
" <td>15.0</td>\n", |
|
|
489 |
" <td>-0.6123</td>\n", |
|
|
490 |
" </tr>\n", |
|
|
491 |
" <tr>\n", |
|
|
492 |
" <th>57966</th>\n", |
|
|
493 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
494 |
" <td>11</td>\n", |
|
|
495 |
" <td>132099856</td>\n", |
|
|
496 |
" <td>134142530</td>\n", |
|
|
497 |
" <td>1010.0</td>\n", |
|
|
498 |
" <td>0.0483</td>\n", |
|
|
499 |
" </tr>\n", |
|
|
500 |
" </tbody>\n", |
|
|
501 |
"</table>\n", |
|
|
502 |
"</div>" |
|
|
503 |
], |
|
|
504 |
"text/plain": [ |
|
|
505 |
" Sample Chromosome Start End \\\n", |
|
|
506 |
"57960 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 456120 64200041 \n", |
|
|
507 |
"57961 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 64208988 64319750 \n", |
|
|
508 |
"57962 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 64325209 126596817 \n", |
|
|
509 |
"57963 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 126596926 127130276 \n", |
|
|
510 |
"57964 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 127132920 132080656 \n", |
|
|
511 |
"57965 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 132080885 132099465 \n", |
|
|
512 |
"57966 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 132099856 134142530 \n", |
|
|
513 |
"\n", |
|
|
514 |
" Num_Probes Segment_Mean \n", |
|
|
515 |
"57960 34710.0 0.0054 \n", |
|
|
516 |
"57961 61.0 -0.6748 \n", |
|
|
517 |
"57962 37207.0 0.0571 \n", |
|
|
518 |
"57963 454.0 -1.0760 \n", |
|
|
519 |
"57964 3591.0 0.0449 \n", |
|
|
520 |
"57965 15.0 -0.6123 \n", |
|
|
521 |
"57966 1010.0 0.0483 " |
|
|
522 |
] |
|
|
523 |
}, |
|
|
524 |
"execution_count": 9, |
|
|
525 |
"metadata": {}, |
|
|
526 |
"output_type": "execute_result" |
|
|
527 |
} |
|
|
528 |
], |
|
|
529 |
"source": [ |
|
|
530 |
"t.loc[t[\"Chromosome\"] ==11,:]" |
|
|
531 |
] |
|
|
532 |
}, |
|
|
533 |
{ |
|
|
534 |
"cell_type": "code", |
|
|
535 |
"execution_count": 10, |
|
|
536 |
"metadata": {}, |
|
|
537 |
"outputs": [ |
|
|
538 |
{ |
|
|
539 |
"name": "stdout", |
|
|
540 |
"output_type": "stream", |
|
|
541 |
"text": [ |
|
|
542 |
"segemtns in normal after dropping low.conf.: 38\n" |
|
|
543 |
] |
|
|
544 |
}, |
|
|
545 |
{ |
|
|
546 |
"data": { |
|
|
547 |
"text/html": [ |
|
|
548 |
"<div>\n", |
|
|
549 |
"<style scoped>\n", |
|
|
550 |
" .dataframe tbody tr th:only-of-type {\n", |
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551 |
" vertical-align: middle;\n", |
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552 |
" }\n", |
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553 |
"\n", |
|
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554 |
" .dataframe tbody tr th {\n", |
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555 |
" vertical-align: top;\n", |
|
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556 |
" }\n", |
|
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557 |
"\n", |
|
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558 |
" .dataframe thead th {\n", |
|
|
559 |
" text-align: right;\n", |
|
|
560 |
" }\n", |
|
|
561 |
"</style>\n", |
|
|
562 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
563 |
" <thead>\n", |
|
|
564 |
" <tr style=\"text-align: right;\">\n", |
|
|
565 |
" <th></th>\n", |
|
|
566 |
" <th>Sample</th>\n", |
|
|
567 |
" <th>Chromosome</th>\n", |
|
|
568 |
" <th>Start</th>\n", |
|
|
569 |
" <th>End</th>\n", |
|
|
570 |
" <th>Num_Probes</th>\n", |
|
|
571 |
" <th>Segment_Mean</th>\n", |
|
|
572 |
" </tr>\n", |
|
|
573 |
" </thead>\n", |
|
|
574 |
" <tbody>\n", |
|
|
575 |
" <tr>\n", |
|
|
576 |
" <th>57804</th>\n", |
|
|
577 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
578 |
" <td>11</td>\n", |
|
|
579 |
" <td>8899400</td>\n", |
|
|
580 |
" <td>8899668</td>\n", |
|
|
581 |
" <td>3.0</td>\n", |
|
|
582 |
" <td>-1.3344</td>\n", |
|
|
583 |
" </tr>\n", |
|
|
584 |
" <tr>\n", |
|
|
585 |
" <th>57806</th>\n", |
|
|
586 |
" <td>TCGA-ZJ-AAXJ-10A-01D-A42Q-01</td>\n", |
|
|
587 |
" <td>11</td>\n", |
|
|
588 |
" <td>126596926</td>\n", |
|
|
589 |
" <td>127130276</td>\n", |
|
|
590 |
" <td>453.0</td>\n", |
|
|
591 |
" <td>-1.0306</td>\n", |
|
|
592 |
" </tr>\n", |
|
|
593 |
" </tbody>\n", |
|
|
594 |
"</table>\n", |
|
|
595 |
"</div>" |
|
|
596 |
], |
|
|
597 |
"text/plain": [ |
|
|
598 |
" Sample Chromosome Start End \\\n", |
|
|
599 |
"57804 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 8899400 8899668 \n", |
|
|
600 |
"57806 TCGA-ZJ-AAXJ-10A-01D-A42Q-01 11 126596926 127130276 \n", |
|
|
601 |
"\n", |
|
|
602 |
" Num_Probes Segment_Mean \n", |
|
|
603 |
"57804 3.0 -1.3344 \n", |
|
|
604 |
"57806 453.0 -1.0306 " |
|
|
605 |
] |
|
|
606 |
}, |
|
|
607 |
"execution_count": 10, |
|
|
608 |
"metadata": {}, |
|
|
609 |
"output_type": "execute_result" |
|
|
610 |
} |
|
|
611 |
], |
|
|
612 |
"source": [ |
|
|
613 |
"n = filter_lowconf_segments(n,0,0.46, -0.68 )\n", |
|
|
614 |
"print(\"segemtns in normal after dropping low.conf.:\",n.shape[0])\n", |
|
|
615 |
"n.loc[n['Chromosome']==11,:]" |
|
|
616 |
] |
|
|
617 |
}, |
|
|
618 |
{ |
|
|
619 |
"cell_type": "code", |
|
|
620 |
"execution_count": 11, |
|
|
621 |
"metadata": {}, |
|
|
622 |
"outputs": [ |
|
|
623 |
{ |
|
|
624 |
"name": "stdout", |
|
|
625 |
"output_type": "stream", |
|
|
626 |
"text": [ |
|
|
627 |
"segemtns in tumor after removing germlines: 194\n" |
|
|
628 |
] |
|
|
629 |
}, |
|
|
630 |
{ |
|
|
631 |
"data": { |
|
|
632 |
"text/html": [ |
|
|
633 |
"<div>\n", |
|
|
634 |
"<style scoped>\n", |
|
|
635 |
" .dataframe tbody tr th:only-of-type {\n", |
|
|
636 |
" vertical-align: middle;\n", |
|
|
637 |
" }\n", |
|
|
638 |
"\n", |
|
|
639 |
" .dataframe tbody tr th {\n", |
|
|
640 |
" vertical-align: top;\n", |
|
|
641 |
" }\n", |
|
|
642 |
"\n", |
|
|
643 |
" .dataframe thead th {\n", |
|
|
644 |
" text-align: right;\n", |
|
|
645 |
" }\n", |
|
|
646 |
"</style>\n", |
|
|
647 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
648 |
" <thead>\n", |
|
|
649 |
" <tr style=\"text-align: right;\">\n", |
|
|
650 |
" <th></th>\n", |
|
|
651 |
" <th>Sample</th>\n", |
|
|
652 |
" <th>Chromosome</th>\n", |
|
|
653 |
" <th>Start</th>\n", |
|
|
654 |
" <th>End</th>\n", |
|
|
655 |
" <th>Num_Probes</th>\n", |
|
|
656 |
" <th>Segment_Mean</th>\n", |
|
|
657 |
" </tr>\n", |
|
|
658 |
" </thead>\n", |
|
|
659 |
" <tbody>\n", |
|
|
660 |
" <tr>\n", |
|
|
661 |
" <th>96</th>\n", |
|
|
662 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
663 |
" <td>11</td>\n", |
|
|
664 |
" <td>456120</td>\n", |
|
|
665 |
" <td>64200041</td>\n", |
|
|
666 |
" <td>34710.0</td>\n", |
|
|
667 |
" <td>0.0054</td>\n", |
|
|
668 |
" </tr>\n", |
|
|
669 |
" <tr>\n", |
|
|
670 |
" <th>97</th>\n", |
|
|
671 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
672 |
" <td>11</td>\n", |
|
|
673 |
" <td>64208988</td>\n", |
|
|
674 |
" <td>64319750</td>\n", |
|
|
675 |
" <td>61.0</td>\n", |
|
|
676 |
" <td>-0.6748</td>\n", |
|
|
677 |
" </tr>\n", |
|
|
678 |
" <tr>\n", |
|
|
679 |
" <th>98</th>\n", |
|
|
680 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
681 |
" <td>11</td>\n", |
|
|
682 |
" <td>64325209</td>\n", |
|
|
683 |
" <td>126596817</td>\n", |
|
|
684 |
" <td>37207.0</td>\n", |
|
|
685 |
" <td>0.0571</td>\n", |
|
|
686 |
" </tr>\n", |
|
|
687 |
" <tr>\n", |
|
|
688 |
" <th>99</th>\n", |
|
|
689 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
690 |
" <td>11</td>\n", |
|
|
691 |
" <td>127132920</td>\n", |
|
|
692 |
" <td>132080656</td>\n", |
|
|
693 |
" <td>3591.0</td>\n", |
|
|
694 |
" <td>0.0449</td>\n", |
|
|
695 |
" </tr>\n", |
|
|
696 |
" <tr>\n", |
|
|
697 |
" <th>100</th>\n", |
|
|
698 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
699 |
" <td>11</td>\n", |
|
|
700 |
" <td>132080885</td>\n", |
|
|
701 |
" <td>132099465</td>\n", |
|
|
702 |
" <td>15.0</td>\n", |
|
|
703 |
" <td>-0.6123</td>\n", |
|
|
704 |
" </tr>\n", |
|
|
705 |
" <tr>\n", |
|
|
706 |
" <th>101</th>\n", |
|
|
707 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
708 |
" <td>11</td>\n", |
|
|
709 |
" <td>132099856</td>\n", |
|
|
710 |
" <td>134142530</td>\n", |
|
|
711 |
" <td>1010.0</td>\n", |
|
|
712 |
" <td>0.0483</td>\n", |
|
|
713 |
" </tr>\n", |
|
|
714 |
" </tbody>\n", |
|
|
715 |
"</table>\n", |
|
|
716 |
"</div>" |
|
|
717 |
], |
|
|
718 |
"text/plain": [ |
|
|
719 |
" Sample Chromosome Start End \\\n", |
|
|
720 |
"96 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 456120 64200041 \n", |
|
|
721 |
"97 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 64208988 64319750 \n", |
|
|
722 |
"98 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 64325209 126596817 \n", |
|
|
723 |
"99 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 127132920 132080656 \n", |
|
|
724 |
"100 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 132080885 132099465 \n", |
|
|
725 |
"101 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 132099856 134142530 \n", |
|
|
726 |
"\n", |
|
|
727 |
" Num_Probes Segment_Mean \n", |
|
|
728 |
"96 34710.0 0.0054 \n", |
|
|
729 |
"97 61.0 -0.6748 \n", |
|
|
730 |
"98 37207.0 0.0571 \n", |
|
|
731 |
"99 3591.0 0.0449 \n", |
|
|
732 |
"100 15.0 -0.6123 \n", |
|
|
733 |
"101 1010.0 0.0483 " |
|
|
734 |
] |
|
|
735 |
}, |
|
|
736 |
"execution_count": 11, |
|
|
737 |
"metadata": {}, |
|
|
738 |
"output_type": "execute_result" |
|
|
739 |
} |
|
|
740 |
], |
|
|
741 |
"source": [ |
|
|
742 |
"\n", |
|
|
743 |
"t = remove_ovelapping_segments(t, n,tumor_barcode)\n", |
|
|
744 |
"print(\"segemtns in tumor after removing germlines:\",t.shape[0])\n", |
|
|
745 |
"t.loc[t[\"Chromosome\"] ==11,:]" |
|
|
746 |
] |
|
|
747 |
}, |
|
|
748 |
{ |
|
|
749 |
"cell_type": "code", |
|
|
750 |
"execution_count": 12, |
|
|
751 |
"metadata": {}, |
|
|
752 |
"outputs": [ |
|
|
753 |
{ |
|
|
754 |
"name": "stdout", |
|
|
755 |
"output_type": "stream", |
|
|
756 |
"text": [ |
|
|
757 |
"segemtns in tumor after dropping low.conf.: 101\n" |
|
|
758 |
] |
|
|
759 |
}, |
|
|
760 |
{ |
|
|
761 |
"data": { |
|
|
762 |
"text/html": [ |
|
|
763 |
"<div>\n", |
|
|
764 |
"<style scoped>\n", |
|
|
765 |
" .dataframe tbody tr th:only-of-type {\n", |
|
|
766 |
" vertical-align: middle;\n", |
|
|
767 |
" }\n", |
|
|
768 |
"\n", |
|
|
769 |
" .dataframe tbody tr th {\n", |
|
|
770 |
" vertical-align: top;\n", |
|
|
771 |
" }\n", |
|
|
772 |
"\n", |
|
|
773 |
" .dataframe thead th {\n", |
|
|
774 |
" text-align: right;\n", |
|
|
775 |
" }\n", |
|
|
776 |
"</style>\n", |
|
|
777 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
778 |
" <thead>\n", |
|
|
779 |
" <tr style=\"text-align: right;\">\n", |
|
|
780 |
" <th></th>\n", |
|
|
781 |
" <th>Sample</th>\n", |
|
|
782 |
" <th>Chromosome</th>\n", |
|
|
783 |
" <th>Start</th>\n", |
|
|
784 |
" <th>End</th>\n", |
|
|
785 |
" <th>Num_Probes</th>\n", |
|
|
786 |
" <th>Segment_Mean</th>\n", |
|
|
787 |
" </tr>\n", |
|
|
788 |
" </thead>\n", |
|
|
789 |
" <tbody>\n", |
|
|
790 |
" <tr>\n", |
|
|
791 |
" <th>97</th>\n", |
|
|
792 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
793 |
" <td>11</td>\n", |
|
|
794 |
" <td>64208988</td>\n", |
|
|
795 |
" <td>64319750</td>\n", |
|
|
796 |
" <td>61.0</td>\n", |
|
|
797 |
" <td>-0.6748</td>\n", |
|
|
798 |
" </tr>\n", |
|
|
799 |
" <tr>\n", |
|
|
800 |
" <th>100</th>\n", |
|
|
801 |
" <td>TCGA-ZJ-AAXJ-01A-11D-A42N-01</td>\n", |
|
|
802 |
" <td>11</td>\n", |
|
|
803 |
" <td>132080885</td>\n", |
|
|
804 |
" <td>132099465</td>\n", |
|
|
805 |
" <td>15.0</td>\n", |
|
|
806 |
" <td>-0.6123</td>\n", |
|
|
807 |
" </tr>\n", |
|
|
808 |
" </tbody>\n", |
|
|
809 |
"</table>\n", |
|
|
810 |
"</div>" |
|
|
811 |
], |
|
|
812 |
"text/plain": [ |
|
|
813 |
" Sample Chromosome Start End \\\n", |
|
|
814 |
"97 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 64208988 64319750 \n", |
|
|
815 |
"100 TCGA-ZJ-AAXJ-01A-11D-A42N-01 11 132080885 132099465 \n", |
|
|
816 |
"\n", |
|
|
817 |
" Num_Probes Segment_Mean \n", |
|
|
818 |
"97 61.0 -0.6748 \n", |
|
|
819 |
"100 15.0 -0.6123 " |
|
|
820 |
] |
|
|
821 |
}, |
|
|
822 |
"execution_count": 12, |
|
|
823 |
"metadata": {}, |
|
|
824 |
"output_type": "execute_result" |
|
|
825 |
} |
|
|
826 |
], |
|
|
827 |
"source": [ |
|
|
828 |
"t = filter_lowconf_segments(t,num_marker_thr,pos_seg_mean_thr, neg_seg_mean_thr )\n", |
|
|
829 |
"print(\"segemtns in tumor after dropping low.conf.:\",t.shape[0])\n", |
|
|
830 |
"t.loc[t[\"Chromosome\"] ==11,:]" |
|
|
831 |
] |
|
|
832 |
}, |
|
|
833 |
{ |
|
|
834 |
"cell_type": "markdown", |
|
|
835 |
"metadata": {}, |
|
|
836 |
"source": [ |
|
|
837 |
"# TCGA " |
|
|
838 |
] |
|
|
839 |
}, |
|
|
840 |
{ |
|
|
841 |
"cell_type": "code", |
|
|
842 |
"execution_count": 14, |
|
|
843 |
"metadata": { |
|
|
844 |
"scrolled": true |
|
|
845 |
}, |
|
|
846 |
"outputs": [ |
|
|
847 |
{ |
|
|
848 |
"name": "stdout", |
|
|
849 |
"output_type": "stream", |
|
|
850 |
"text": [ |
|
|
851 |
"HNSC samples: 1089 CNA events per sample on avg.: 101.275482094\n" |
|
|
852 |
] |
|
|
853 |
}, |
|
|
854 |
{ |
|
|
855 |
"name": "stderr", |
|
|
856 |
"output_type": "stream", |
|
|
857 |
"text": [ |
|
|
858 |
"total samples: 1089 tumors: 530 normals: 559\n", |
|
|
859 |
"\ttumors without matched normal 28\n", |
|
|
860 |
"\ttumors with at least one sCNA 497\n", |
|
|
861 |
"\ttumors without any somatic CNA 5\n" |
|
|
862 |
] |
|
|
863 |
}, |
|
|
864 |
{ |
|
|
865 |
"name": "stdout", |
|
|
866 |
"output_type": "stream", |
|
|
867 |
"text": [ |
|
|
868 |
"after filtering\n", |
|
|
869 |
"HNSC samples: 525 Segments per sample on avg.: 60.6876190476\n", |
|
|
870 |
"ESCA samples: 373 CNA events per sample on avg.: 163.010723861\n" |
|
|
871 |
] |
|
|
872 |
}, |
|
|
873 |
{ |
|
|
874 |
"name": "stderr", |
|
|
875 |
"output_type": "stream", |
|
|
876 |
"text": [ |
|
|
877 |
"total samples: 373 tumors: 185 normals: 188\n", |
|
|
878 |
"\ttumors without matched normal 3\n", |
|
|
879 |
"\ttumors with at least one sCNA 181\n", |
|
|
880 |
"\ttumors without any somatic CNA 1\n", |
|
|
881 |
"total samples: 248 tumors: 125 normals: 123\n" |
|
|
882 |
] |
|
|
883 |
}, |
|
|
884 |
{ |
|
|
885 |
"name": "stdout", |
|
|
886 |
"output_type": "stream", |
|
|
887 |
"text": [ |
|
|
888 |
"after filtering\n", |
|
|
889 |
"ESCA samples: 184 Segments per sample on avg.: 141.836956522\n", |
|
|
890 |
"THYM samples: 248 CNA events per sample on avg.: 62.7862903226\n" |
|
|
891 |
] |
|
|
892 |
}, |
|
|
893 |
{ |
|
|
894 |
"name": "stderr", |
|
|
895 |
"output_type": "stream", |
|
|
896 |
"text": [ |
|
|
897 |
"\ttumors without matched normal 5\n", |
|
|
898 |
"\ttumors with at least one sCNA 95\n", |
|
|
899 |
"\ttumors without any somatic CNA 25\n", |
|
|
900 |
"total samples: 132 tumors: 66 normals: 66\n" |
|
|
901 |
] |
|
|
902 |
}, |
|
|
903 |
{ |
|
|
904 |
"name": "stdout", |
|
|
905 |
"output_type": "stream", |
|
|
906 |
"text": [ |
|
|
907 |
"after filtering\n", |
|
|
908 |
"THYM samples: 100 Segments per sample on avg.: 9.41\n", |
|
|
909 |
"KICH samples: 132 CNA events per sample on avg.: 77.0\n" |
|
|
910 |
] |
|
|
911 |
}, |
|
|
912 |
{ |
|
|
913 |
"name": "stderr", |
|
|
914 |
"output_type": "stream", |
|
|
915 |
"text": [ |
|
|
916 |
"\ttumors without matched normal 0\n", |
|
|
917 |
"\ttumors with at least one sCNA 65\n", |
|
|
918 |
"\ttumors without any somatic CNA 1\n" |
|
|
919 |
] |
|
|
920 |
}, |
|
|
921 |
{ |
|
|
922 |
"name": "stdout", |
|
|
923 |
"output_type": "stream", |
|
|
924 |
"text": [ |
|
|
925 |
"after filtering\n", |
|
|
926 |
"KICH samples: 65 Segments per sample on avg.: 51.4923076923\n", |
|
|
927 |
"LUSC samples: 1032 CNA events per sample on avg.: 130.682170543\n" |
|
|
928 |
] |
|
|
929 |
}, |
|
|
930 |
{ |
|
|
931 |
"name": "stderr", |
|
|
932 |
"output_type": "stream", |
|
|
933 |
"text": [ |
|
|
934 |
"total samples: 1032 tumors: 501 normals: 531\n", |
|
|
935 |
"\ttumors without matched normal 23\n", |
|
|
936 |
"\ttumors with at least one sCNA 476\n", |
|
|
937 |
"\ttumors without any somatic CNA 2\n" |
|
|
938 |
] |
|
|
939 |
}, |
|
|
940 |
{ |
|
|
941 |
"name": "stdout", |
|
|
942 |
"output_type": "stream", |
|
|
943 |
"text": [ |
|
|
944 |
"after filtering\n", |
|
|
945 |
"LUSC samples: 499 Segments per sample on avg.: 94.6533066132\n", |
|
|
946 |
"BLCA samples: 797 CNA events per sample on avg.: 130.927227102\n" |
|
|
947 |
] |
|
|
948 |
}, |
|
|
949 |
{ |
|
|
950 |
"name": "stderr", |
|
|
951 |
"output_type": "stream", |
|
|
952 |
"text": [ |
|
|
953 |
"total samples: 797 tumors: 414 normals: 383\n", |
|
|
954 |
"\ttumors without matched normal 46\n", |
|
|
955 |
"\ttumors with at least one sCNA 366\n", |
|
|
956 |
"\ttumors without any somatic CNA 2\n" |
|
|
957 |
] |
|
|
958 |
}, |
|
|
959 |
{ |
|
|
960 |
"name": "stdout", |
|
|
961 |
"output_type": "stream", |
|
|
962 |
"text": [ |
|
|
963 |
"after filtering\n", |
|
|
964 |
"BLCA samples: 412 Segments per sample on avg.: 94.8859223301\n", |
|
|
965 |
"GBM samples: 1104 CNA events per sample on avg.: 133.018115942\n" |
|
|
966 |
] |
|
|
967 |
}, |
|
|
968 |
{ |
|
|
969 |
"name": "stderr", |
|
|
970 |
"output_type": "stream", |
|
|
971 |
"text": [ |
|
|
972 |
"total samples: 1104 tumors: 590 normals: 514\n", |
|
|
973 |
"\ttumors without matched normal 78\n", |
|
|
974 |
"\ttumors with at least one sCNA 511\n", |
|
|
975 |
"\ttumors without any somatic CNA 1\n", |
|
|
976 |
"total samples: 85 tumors: 36 normals: 49\n" |
|
|
977 |
] |
|
|
978 |
}, |
|
|
979 |
{ |
|
|
980 |
"name": "stdout", |
|
|
981 |
"output_type": "stream", |
|
|
982 |
"text": [ |
|
|
983 |
"after filtering\n", |
|
|
984 |
"GBM samples: 589 Segments per sample on avg.: 70.2139219015\n", |
|
|
985 |
"CHOL samples: 85 CNA events per sample on avg.: 89.0588235294\n" |
|
|
986 |
] |
|
|
987 |
}, |
|
|
988 |
{ |
|
|
989 |
"name": "stderr", |
|
|
990 |
"output_type": "stream", |
|
|
991 |
"text": [ |
|
|
992 |
"\ttumors without matched normal 0\n", |
|
|
993 |
"\ttumors with at least one sCNA 36\n", |
|
|
994 |
"\ttumors without any somatic CNA 0\n", |
|
|
995 |
"total samples: 111 tumors: 56 normals: 55\n" |
|
|
996 |
] |
|
|
997 |
}, |
|
|
998 |
{ |
|
|
999 |
"name": "stdout", |
|
|
1000 |
"output_type": "stream", |
|
|
1001 |
"text": [ |
|
|
1002 |
"after filtering\n", |
|
|
1003 |
"CHOL samples: 36 Segments per sample on avg.: 56.6944444444\n", |
|
|
1004 |
"UCS samples: 111 CNA events per sample on avg.: 173.855855856\n" |
|
|
1005 |
] |
|
|
1006 |
}, |
|
|
1007 |
{ |
|
|
1008 |
"name": "stderr", |
|
|
1009 |
"output_type": "stream", |
|
|
1010 |
"text": [ |
|
|
1011 |
"\ttumors without matched normal 2\n", |
|
|
1012 |
"\ttumors with at least one sCNA 54\n", |
|
|
1013 |
"\ttumors without any somatic CNA 0\n" |
|
|
1014 |
] |
|
|
1015 |
}, |
|
|
1016 |
{ |
|
|
1017 |
"name": "stdout", |
|
|
1018 |
"output_type": "stream", |
|
|
1019 |
"text": [ |
|
|
1020 |
"after filtering\n", |
|
|
1021 |
"UCS samples: 56 Segments per sample on avg.: 179.125\n", |
|
|
1022 |
"LGG samples: 1015 CNA events per sample on avg.: 78.6118226601\n" |
|
|
1023 |
] |
|
|
1024 |
}, |
|
|
1025 |
{ |
|
|
1026 |
"name": "stderr", |
|
|
1027 |
"output_type": "stream", |
|
|
1028 |
"text": [ |
|
|
1029 |
"total samples: 1015 tumors: 530 normals: 485\n", |
|
|
1030 |
"\ttumors without matched normal 33\n", |
|
|
1031 |
"\ttumors with at least one sCNA 494\n", |
|
|
1032 |
"\ttumors without any somatic CNA 3\n" |
|
|
1033 |
] |
|
|
1034 |
}, |
|
|
1035 |
{ |
|
|
1036 |
"name": "stdout", |
|
|
1037 |
"output_type": "stream", |
|
|
1038 |
"text": [ |
|
|
1039 |
"after filtering\n", |
|
|
1040 |
"LGG samples: 527 Segments per sample on avg.: 29.1157495256\n", |
|
|
1041 |
"THCA samples: 1013 CNA events per sample on avg.: 54.4096742349\n" |
|
|
1042 |
] |
|
|
1043 |
}, |
|
|
1044 |
{ |
|
|
1045 |
"name": "stderr", |
|
|
1046 |
"output_type": "stream", |
|
|
1047 |
"text": [ |
|
|
1048 |
"total samples: 1013 tumors: 506 normals: 507\n", |
|
|
1049 |
"\ttumors without matched normal 15\n", |
|
|
1050 |
"\ttumors with at least one sCNA 367\n", |
|
|
1051 |
"\ttumors without any somatic CNA 124\n", |
|
|
1052 |
"total samples: 365 tumors: 185 normals: 180\n" |
|
|
1053 |
] |
|
|
1054 |
}, |
|
|
1055 |
{ |
|
|
1056 |
"name": "stdout", |
|
|
1057 |
"output_type": "stream", |
|
|
1058 |
"text": [ |
|
|
1059 |
"after filtering\n", |
|
|
1060 |
"THCA samples: 382 Segments per sample on avg.: 3.8219895288\n", |
|
|
1061 |
"PAAD samples: 365 CNA events per sample on avg.: 95.3643835616\n" |
|
|
1062 |
] |
|
|
1063 |
}, |
|
|
1064 |
{ |
|
|
1065 |
"name": "stderr", |
|
|
1066 |
"output_type": "stream", |
|
|
1067 |
"text": [ |
|
|
1068 |
"\ttumors without matched normal 10\n", |
|
|
1069 |
"\ttumors with at least one sCNA 161\n", |
|
|
1070 |
"\ttumors without any somatic CNA 14\n", |
|
|
1071 |
"total samples: 1059 tumors: 529 normals: 530\n" |
|
|
1072 |
] |
|
|
1073 |
}, |
|
|
1074 |
{ |
|
|
1075 |
"name": "stdout", |
|
|
1076 |
"output_type": "stream", |
|
|
1077 |
"text": [ |
|
|
1078 |
"after filtering\n", |
|
|
1079 |
"PAAD samples: 171 Segments per sample on avg.: 32.4093567251\n", |
|
|
1080 |
"KIRC samples: 1059 CNA events per sample on avg.: 80.298394712\n" |
|
|
1081 |
] |
|
|
1082 |
}, |
|
|
1083 |
{ |
|
|
1084 |
"name": "stderr", |
|
|
1085 |
"output_type": "stream", |
|
|
1086 |
"text": [ |
|
|
1087 |
"\ttumors without matched normal 22\n", |
|
|
1088 |
"\ttumors with at least one sCNA 501\n", |
|
|
1089 |
"\ttumors without any somatic CNA 6\n", |
|
|
1090 |
"total samples: 160 tumors: 80 normals: 80\n" |
|
|
1091 |
] |
|
|
1092 |
}, |
|
|
1093 |
{ |
|
|
1094 |
"name": "stdout", |
|
|
1095 |
"output_type": "stream", |
|
|
1096 |
"text": [ |
|
|
1097 |
"after filtering\n", |
|
|
1098 |
"KIRC samples: 523 Segments per sample on avg.: 20.5009560229\n", |
|
|
1099 |
"UVM samples: 160 CNA events per sample on avg.: 81.08125\n" |
|
|
1100 |
] |
|
|
1101 |
}, |
|
|
1102 |
{ |
|
|
1103 |
"name": "stderr", |
|
|
1104 |
"output_type": "stream", |
|
|
1105 |
"text": [ |
|
|
1106 |
"\ttumors without matched normal 0\n", |
|
|
1107 |
"\ttumors with at least one sCNA 80\n", |
|
|
1108 |
"\ttumors without any somatic CNA 0\n", |
|
|
1109 |
"total samples: 586 tumors: 297 normals: 289\n" |
|
|
1110 |
] |
|
|
1111 |
}, |
|
|
1112 |
{ |
|
|
1113 |
"name": "stdout", |
|
|
1114 |
"output_type": "stream", |
|
|
1115 |
"text": [ |
|
|
1116 |
"after filtering\n", |
|
|
1117 |
"UVM samples: 80 Segments per sample on avg.: 38.425\n", |
|
|
1118 |
"CESC samples: 586 CNA events per sample on avg.: 101.450511945\n" |
|
|
1119 |
] |
|
|
1120 |
}, |
|
|
1121 |
{ |
|
|
1122 |
"name": "stderr", |
|
|
1123 |
"output_type": "stream", |
|
|
1124 |
"text": [ |
|
|
1125 |
"\ttumors without matched normal 16\n", |
|
|
1126 |
"\ttumors with at least one sCNA 280\n", |
|
|
1127 |
"\ttumors without any somatic CNA 1\n" |
|
|
1128 |
] |
|
|
1129 |
}, |
|
|
1130 |
{ |
|
|
1131 |
"name": "stdout", |
|
|
1132 |
"output_type": "stream", |
|
|
1133 |
"text": [ |
|
|
1134 |
"after filtering\n", |
|
|
1135 |
"CESC samples: 296 Segments per sample on avg.: 58.1351351351\n", |
|
|
1136 |
"LUAD samples: 1095 CNA events per sample on avg.: 105.78630137\n" |
|
|
1137 |
] |
|
|
1138 |
}, |
|
|
1139 |
{ |
|
|
1140 |
"name": "stderr", |
|
|
1141 |
"output_type": "stream", |
|
|
1142 |
"text": [ |
|
|
1143 |
"total samples: 1095 tumors: 518 normals: 577\n", |
|
|
1144 |
"\ttumors without matched normal 19\n", |
|
|
1145 |
"\ttumors with at least one sCNA 494\n", |
|
|
1146 |
"\ttumors without any somatic CNA 5\n" |
|
|
1147 |
] |
|
|
1148 |
}, |
|
|
1149 |
{ |
|
|
1150 |
"name": "stdout", |
|
|
1151 |
"output_type": "stream", |
|
|
1152 |
"text": [ |
|
|
1153 |
"after filtering\n", |
|
|
1154 |
"LUAD samples: 513 Segments per sample on avg.: 70.469785575\n", |
|
|
1155 |
"STAD samples: 904 CNA events per sample on avg.: 130.961283186\n" |
|
|
1156 |
] |
|
|
1157 |
}, |
|
|
1158 |
{ |
|
|
1159 |
"name": "stderr", |
|
|
1160 |
"output_type": "stream", |
|
|
1161 |
"text": [ |
|
|
1162 |
"total samples: 904 tumors: 442 normals: 462\n", |
|
|
1163 |
"\ttumors without matched normal 26\n", |
|
|
1164 |
"\ttumors with at least one sCNA 410\n", |
|
|
1165 |
"\ttumors without any somatic CNA 6\n" |
|
|
1166 |
] |
|
|
1167 |
}, |
|
|
1168 |
{ |
|
|
1169 |
"name": "stdout", |
|
|
1170 |
"output_type": "stream", |
|
|
1171 |
"text": [ |
|
|
1172 |
"after filtering\n", |
|
|
1173 |
"STAD samples: 436 Segments per sample on avg.: 96.4220183486\n", |
|
|
1174 |
"UCEC samples: 1089 CNA events per sample on avg.: 116.707070707\n" |
|
|
1175 |
] |
|
|
1176 |
}, |
|
|
1177 |
{ |
|
|
1178 |
"name": "stderr", |
|
|
1179 |
"output_type": "stream", |
|
|
1180 |
"text": [ |
|
|
1181 |
"total samples: 1089 tumors: 540 normals: 549\n", |
|
|
1182 |
"\ttumors without matched normal 23\n", |
|
|
1183 |
"\ttumors with at least one sCNA 504\n", |
|
|
1184 |
"\ttumors without any somatic CNA 13\n" |
|
|
1185 |
] |
|
|
1186 |
}, |
|
|
1187 |
{ |
|
|
1188 |
"name": "stdout", |
|
|
1189 |
"output_type": "stream", |
|
|
1190 |
"text": [ |
|
|
1191 |
"after filtering\n", |
|
|
1192 |
"UCEC samples: 527 Segments per sample on avg.: 78.89943074\n", |
|
|
1193 |
"SKCM samples: 937 CNA events per sample on avg.: 115.351120598\n" |
|
|
1194 |
] |
|
|
1195 |
}, |
|
|
1196 |
{ |
|
|
1197 |
"name": "stderr", |
|
|
1198 |
"output_type": "stream", |
|
|
1199 |
"text": [ |
|
|
1200 |
"total samples: 937 tumors: 472 normals: 465\n", |
|
|
1201 |
"\ttumors without matched normal 7\n", |
|
|
1202 |
"\ttumors with at least one sCNA 463\n", |
|
|
1203 |
"\ttumors without any somatic CNA 2\n", |
|
|
1204 |
"total samples: 172 tumors: 87 normals: 85\n" |
|
|
1205 |
] |
|
|
1206 |
}, |
|
|
1207 |
{ |
|
|
1208 |
"name": "stdout", |
|
|
1209 |
"output_type": "stream", |
|
|
1210 |
"text": [ |
|
|
1211 |
"after filtering\n", |
|
|
1212 |
"SKCM samples: 470 Segments per sample on avg.: 82.9957446809\n", |
|
|
1213 |
"MESO samples: 172 CNA events per sample on avg.: 106.598837209\n" |
|
|
1214 |
] |
|
|
1215 |
}, |
|
|
1216 |
{ |
|
|
1217 |
"name": "stderr", |
|
|
1218 |
"output_type": "stream", |
|
|
1219 |
"text": [ |
|
|
1220 |
"\ttumors without matched normal 2\n", |
|
|
1221 |
"\ttumors with at least one sCNA 82\n", |
|
|
1222 |
"\ttumors without any somatic CNA 3\n", |
|
|
1223 |
"total samples: 346 tumors: 168 normals: 178\n" |
|
|
1224 |
] |
|
|
1225 |
}, |
|
|
1226 |
{ |
|
|
1227 |
"name": "stdout", |
|
|
1228 |
"output_type": "stream", |
|
|
1229 |
"text": [ |
|
|
1230 |
"after filtering\n", |
|
|
1231 |
"MESO samples: 84 Segments per sample on avg.: 60.8333333333\n", |
|
|
1232 |
"PCPG samples: 346 CNA events per sample on avg.: 90.3352601156\n" |
|
|
1233 |
] |
|
|
1234 |
}, |
|
|
1235 |
{ |
|
|
1236 |
"name": "stderr", |
|
|
1237 |
"output_type": "stream", |
|
|
1238 |
"text": [ |
|
|
1239 |
"\ttumors without matched normal 6\n", |
|
|
1240 |
"\ttumors with at least one sCNA 159\n", |
|
|
1241 |
"\ttumors without any somatic CNA 3\n" |
|
|
1242 |
] |
|
|
1243 |
}, |
|
|
1244 |
{ |
|
|
1245 |
"name": "stdout", |
|
|
1246 |
"output_type": "stream", |
|
|
1247 |
"text": [ |
|
|
1248 |
"after filtering\n", |
|
|
1249 |
"PCPG samples: 165 Segments per sample on avg.: 43.5878787879\n", |
|
|
1250 |
"STES samples: 1277 CNA events per sample on avg.: 140.322631167\n" |
|
|
1251 |
] |
|
|
1252 |
}, |
|
|
1253 |
{ |
|
|
1254 |
"name": "stderr", |
|
|
1255 |
"output_type": "stream", |
|
|
1256 |
"text": [ |
|
|
1257 |
"total samples: 1277 tumors: 627 normals: 650\n", |
|
|
1258 |
"\ttumors without matched normal 29\n", |
|
|
1259 |
"\ttumors with at least one sCNA 591\n", |
|
|
1260 |
"\ttumors without any somatic CNA 7\n" |
|
|
1261 |
] |
|
|
1262 |
}, |
|
|
1263 |
{ |
|
|
1264 |
"name": "stdout", |
|
|
1265 |
"output_type": "stream", |
|
|
1266 |
"text": [ |
|
|
1267 |
"after filtering\n", |
|
|
1268 |
"STES samples: 620 Segments per sample on avg.: 109.9\n", |
|
|
1269 |
"SARC samples: 513 CNA events per sample on avg.: 208.068226121\n" |
|
|
1270 |
] |
|
|
1271 |
}, |
|
|
1272 |
{ |
|
|
1273 |
"name": "stderr", |
|
|
1274 |
"output_type": "stream", |
|
|
1275 |
"text": [ |
|
|
1276 |
"total samples: 513 tumors: 263 normals: 250\n", |
|
|
1277 |
"\ttumors without matched normal 17\n", |
|
|
1278 |
"\ttumors with at least one sCNA 245\n", |
|
|
1279 |
"\ttumors without any somatic CNA 1\n", |
|
|
1280 |
"total samples: 380 tumors: 191 normals: 189\n" |
|
|
1281 |
] |
|
|
1282 |
}, |
|
|
1283 |
{ |
|
|
1284 |
"name": "stdout", |
|
|
1285 |
"output_type": "stream", |
|
|
1286 |
"text": [ |
|
|
1287 |
"after filtering\n", |
|
|
1288 |
"SARC samples: 262 Segments per sample on avg.: 187.057251908\n", |
|
|
1289 |
"LAML samples: 380 CNA events per sample on avg.: 74.5368421053\n" |
|
|
1290 |
] |
|
|
1291 |
}, |
|
|
1292 |
{ |
|
|
1293 |
"name": "stderr", |
|
|
1294 |
"output_type": "stream", |
|
|
1295 |
"text": [ |
|
|
1296 |
"\ttumors without matched normal 3\n", |
|
|
1297 |
"\ttumors with at least one sCNA 167\n", |
|
|
1298 |
"\ttumors without any somatic CNA 21\n", |
|
|
1299 |
"total samples: 590 tumors: 288 normals: 302\n" |
|
|
1300 |
] |
|
|
1301 |
}, |
|
|
1302 |
{ |
|
|
1303 |
"name": "stdout", |
|
|
1304 |
"output_type": "stream", |
|
|
1305 |
"text": [ |
|
|
1306 |
"after filtering\n", |
|
|
1307 |
"LAML samples: 170 Segments per sample on avg.: 7.18823529412\n", |
|
|
1308 |
"KIRP samples: 590 CNA events per sample on avg.: 79.5152542373\n" |
|
|
1309 |
] |
|
|
1310 |
}, |
|
|
1311 |
{ |
|
|
1312 |
"name": "stderr", |
|
|
1313 |
"output_type": "stream", |
|
|
1314 |
"text": [ |
|
|
1315 |
"\ttumors without matched normal 15\n", |
|
|
1316 |
"\ttumors with at least one sCNA 271\n", |
|
|
1317 |
"\ttumors without any somatic CNA 2\n" |
|
|
1318 |
] |
|
|
1319 |
}, |
|
|
1320 |
{ |
|
|
1321 |
"name": "stdout", |
|
|
1322 |
"output_type": "stream", |
|
|
1323 |
"text": [ |
|
|
1324 |
"after filtering\n", |
|
|
1325 |
"KIRP samples: 286 Segments per sample on avg.: 21.8846153846\n", |
|
|
1326 |
"LIHC samples: 760 CNA events per sample on avg.: 122.8\n" |
|
|
1327 |
] |
|
|
1328 |
}, |
|
|
1329 |
{ |
|
|
1330 |
"name": "stderr", |
|
|
1331 |
"output_type": "stream", |
|
|
1332 |
"text": [ |
|
|
1333 |
"total samples: 760 tumors: 373 normals: 387\n", |
|
|
1334 |
"\ttumors without matched normal 21\n", |
|
|
1335 |
"\ttumors with at least one sCNA 348\n", |
|
|
1336 |
"\ttumors without any somatic CNA 4\n" |
|
|
1337 |
] |
|
|
1338 |
}, |
|
|
1339 |
{ |
|
|
1340 |
"name": "stdout", |
|
|
1341 |
"output_type": "stream", |
|
|
1342 |
"text": [ |
|
|
1343 |
"after filtering\n", |
|
|
1344 |
"LIHC samples: 369 Segments per sample on avg.: 81.1327913279\n", |
|
|
1345 |
"OV samples: 1168 CNA events per sample on avg.: 224.04109589\n" |
|
|
1346 |
] |
|
|
1347 |
}, |
|
|
1348 |
{ |
|
|
1349 |
"name": "stderr", |
|
|
1350 |
"output_type": "stream", |
|
|
1351 |
"text": [ |
|
|
1352 |
"total samples: 1168 tumors: 597 normals: 571\n", |
|
|
1353 |
"\ttumors without matched normal 26\n", |
|
|
1354 |
"\ttumors with at least one sCNA 571\n", |
|
|
1355 |
"\ttumors without any somatic CNA 0\n" |
|
|
1356 |
] |
|
|
1357 |
}, |
|
|
1358 |
{ |
|
|
1359 |
"name": "stdout", |
|
|
1360 |
"output_type": "stream", |
|
|
1361 |
"text": [ |
|
|
1362 |
"after filtering\n", |
|
|
1363 |
"OV samples: 597 Segments per sample on avg.: 207.924623116\n", |
|
|
1364 |
"TGCT samples: 304 CNA events per sample on avg.: 83.8125\n" |
|
|
1365 |
] |
|
|
1366 |
}, |
|
|
1367 |
{ |
|
|
1368 |
"name": "stderr", |
|
|
1369 |
"output_type": "stream", |
|
|
1370 |
"text": [ |
|
|
1371 |
"total samples: 304 tumors: 156 normals: 148\n", |
|
|
1372 |
"\ttumors without matched normal 2\n", |
|
|
1373 |
"\ttumors with at least one sCNA 154\n", |
|
|
1374 |
"\ttumors without any somatic CNA 0\n" |
|
|
1375 |
] |
|
|
1376 |
}, |
|
|
1377 |
{ |
|
|
1378 |
"name": "stdout", |
|
|
1379 |
"output_type": "stream", |
|
|
1380 |
"text": [ |
|
|
1381 |
"after filtering\n", |
|
|
1382 |
"TGCT samples: 156 Segments per sample on avg.: 37.7820512821\n", |
|
|
1383 |
"COAD samples: 918 CNA events per sample on avg.: 98.6209150327\n" |
|
|
1384 |
] |
|
|
1385 |
}, |
|
|
1386 |
{ |
|
|
1387 |
"name": "stderr", |
|
|
1388 |
"output_type": "stream", |
|
|
1389 |
"text": [ |
|
|
1390 |
"total samples: 918 tumors: 453 normals: 465\n", |
|
|
1391 |
"\ttumors without matched normal 44\n", |
|
|
1392 |
"\ttumors with at least one sCNA 406\n", |
|
|
1393 |
"\ttumors without any somatic CNA 3\n" |
|
|
1394 |
] |
|
|
1395 |
}, |
|
|
1396 |
{ |
|
|
1397 |
"name": "stdout", |
|
|
1398 |
"output_type": "stream", |
|
|
1399 |
"text": [ |
|
|
1400 |
"after filtering\n", |
|
|
1401 |
"COAD samples: 450 Segments per sample on avg.: 48.4755555556\n", |
|
|
1402 |
"BRCA samples: 2199 CNA events per sample on avg.: 129.35788995\n" |
|
|
1403 |
] |
|
|
1404 |
}, |
|
|
1405 |
{ |
|
|
1406 |
"name": "stderr", |
|
|
1407 |
"output_type": "stream", |
|
|
1408 |
"text": [ |
|
|
1409 |
"total samples: 2199 tumors: 1088 normals: 1111\n", |
|
|
1410 |
"\ttumors without matched normal 35\n", |
|
|
1411 |
"\ttumors with at least one sCNA 1046\n", |
|
|
1412 |
"\ttumors without any somatic CNA 7\n" |
|
|
1413 |
] |
|
|
1414 |
}, |
|
|
1415 |
{ |
|
|
1416 |
"name": "stdout", |
|
|
1417 |
"output_type": "stream", |
|
|
1418 |
"text": [ |
|
|
1419 |
"after filtering\n", |
|
|
1420 |
"BRCA samples: 1081 Segments per sample on avg.: 102.808510638\n", |
|
|
1421 |
"PRAD samples: 1023 CNA events per sample on avg.: 114.706744868\n" |
|
|
1422 |
] |
|
|
1423 |
}, |
|
|
1424 |
{ |
|
|
1425 |
"name": "stderr", |
|
|
1426 |
"output_type": "stream", |
|
|
1427 |
"text": [ |
|
|
1428 |
"total samples: 1023 tumors: 493 normals: 530\n", |
|
|
1429 |
"\ttumors without matched normal 17\n", |
|
|
1430 |
"\ttumors with at least one sCNA 458\n", |
|
|
1431 |
"\ttumors without any somatic CNA 18\n", |
|
|
1432 |
"total samples: 96 tumors: 52 normals: 44\n" |
|
|
1433 |
] |
|
|
1434 |
}, |
|
|
1435 |
{ |
|
|
1436 |
"name": "stdout", |
|
|
1437 |
"output_type": "stream", |
|
|
1438 |
"text": [ |
|
|
1439 |
"after filtering\n", |
|
|
1440 |
"PRAD samples: 475 Segments per sample on avg.: 60.3831578947\n", |
|
|
1441 |
"DLBC samples: 96 CNA events per sample on avg.: 97.3229166667\n" |
|
|
1442 |
] |
|
|
1443 |
}, |
|
|
1444 |
{ |
|
|
1445 |
"name": "stderr", |
|
|
1446 |
"output_type": "stream", |
|
|
1447 |
"text": [ |
|
|
1448 |
"\ttumors without matched normal 10\n", |
|
|
1449 |
"\ttumors with at least one sCNA 40\n", |
|
|
1450 |
"\ttumors without any somatic CNA 2\n" |
|
|
1451 |
] |
|
|
1452 |
}, |
|
|
1453 |
{ |
|
|
1454 |
"name": "stdout", |
|
|
1455 |
"output_type": "stream", |
|
|
1456 |
"text": [ |
|
|
1457 |
"after filtering\n", |
|
|
1458 |
"DLBC samples: 50 Segments per sample on avg.: 44.44\n", |
|
|
1459 |
"READ samples: 316 CNA events per sample on avg.: 113.180379747\n" |
|
|
1460 |
] |
|
|
1461 |
}, |
|
|
1462 |
{ |
|
|
1463 |
"name": "stderr", |
|
|
1464 |
"output_type": "stream", |
|
|
1465 |
"text": [ |
|
|
1466 |
"total samples: 316 tumors: 166 normals: 150\n", |
|
|
1467 |
"\ttumors without matched normal 23\n", |
|
|
1468 |
"\ttumors with at least one sCNA 141\n", |
|
|
1469 |
"\ttumors without any somatic CNA 2\n" |
|
|
1470 |
] |
|
|
1471 |
}, |
|
|
1472 |
{ |
|
|
1473 |
"name": "stdout", |
|
|
1474 |
"output_type": "stream", |
|
|
1475 |
"text": [ |
|
|
1476 |
"after filtering\n", |
|
|
1477 |
"READ samples: 164 Segments per sample on avg.: 70.012195122\n", |
|
|
1478 |
"ACC samples: 180 CNA events per sample on avg.: 116.955555556\n" |
|
|
1479 |
] |
|
|
1480 |
}, |
|
|
1481 |
{ |
|
|
1482 |
"name": "stderr", |
|
|
1483 |
"output_type": "stream", |
|
|
1484 |
"text": [ |
|
|
1485 |
"total samples: 180 tumors: 90 normals: 90\n" |
|
|
1486 |
] |
|
|
1487 |
}, |
|
|
1488 |
{ |
|
|
1489 |
"name": "stdout", |
|
|
1490 |
"output_type": "stream", |
|
|
1491 |
"text": [ |
|
|
1492 |
"after filtering\n", |
|
|
1493 |
"ACC samples: 89 Segments per sample on avg.: 107.449438202\n" |
|
|
1494 |
] |
|
|
1495 |
}, |
|
|
1496 |
{ |
|
|
1497 |
"name": "stderr", |
|
|
1498 |
"output_type": "stream", |
|
|
1499 |
"text": [ |
|
|
1500 |
"\ttumors without matched normal 2\n", |
|
|
1501 |
"\ttumors with at least one sCNA 87\n", |
|
|
1502 |
"\ttumors without any somatic CNA 1\n" |
|
|
1503 |
] |
|
|
1504 |
} |
|
|
1505 |
], |
|
|
1506 |
"source": [ |
|
|
1507 |
"\n", |
|
|
1508 |
"data_dir = \"../../TCGA/CNA/data__2016_01_28//\"\n", |
|
|
1509 |
"\n", |
|
|
1510 |
"dfs = {}\n", |
|
|
1511 |
"dfs_normals = {}\n", |
|
|
1512 |
"tumors_without_CNA = {}\n", |
|
|
1513 |
"for f in os.listdir(data_dir):\n", |
|
|
1514 |
" if f.endswith(\"tar.gz\"):\n", |
|
|
1515 |
" fp = f.replace(\".tar.gz\",\"\")\n", |
|
|
1516 |
" cohort = fp.split(\".\")[2].replace(\"org_\",\"\")\n", |
|
|
1517 |
" file_path = fp+\"/\"+cohort+\".\"+fp.split(\".\")[3].replace(\"Merge_\",\"\")+\".seg.txt\"\n", |
|
|
1518 |
" df = pd.read_csv(data_dir+file_path, sep = \"\\t\")\n", |
|
|
1519 |
" \n", |
|
|
1520 |
" df[\"Chromosome\"] = df[\"Chromosome\"].map(chr_dict)\n", |
|
|
1521 |
" print(cohort,\"samples:\",len(set(df[\"Sample\"].values)),\n", |
|
|
1522 |
" \"CNA events per sample on avg.:\",float(df.shape[0])/len(set(df[\"Sample\"].values)))\n", |
|
|
1523 |
" \n", |
|
|
1524 |
" #### remove segments overlapping with segemnts in normals by 80% or more reciprocally ####\n", |
|
|
1525 |
" df[\"type\"] = df[\"Sample\"].apply(sample_type)\n", |
|
|
1526 |
" df_normals = df.loc[df[\"type\"]== \"Normal\",[\"Sample\",\"Chromosome\",\"Start\",\"End\",\"Num_Probes\",\"Segment_Mean\"]]\n", |
|
|
1527 |
" df_tumors = df.loc[df[\"type\"]== \"Tumor\",[\"Sample\",\"Chromosome\",\"Start\",\"End\",\"Num_Probes\",\"Segment_Mean\"]]\n", |
|
|
1528 |
" normal_samples = list(set(df_normals[\"Sample\"].values))\n", |
|
|
1529 |
" tumor_samples = list(set(df_tumors[\"Sample\"].values))\n", |
|
|
1530 |
" print(\"total samples:\", len(set(df[\"Sample\"].values)),\n", |
|
|
1531 |
" \"tumors:\",len(tumor_samples),\"normals:\",len(normal_samples),file= sys.stderr)\n", |
|
|
1532 |
" \n", |
|
|
1533 |
" tumors_without_somatic_CNA = []\n", |
|
|
1534 |
" tumors_germline_removed = []\n", |
|
|
1535 |
" tumors_without_matching_normal = []\n", |
|
|
1536 |
" filtered_normals = []\n", |
|
|
1537 |
" for tumor_sample in tumor_samples:\n", |
|
|
1538 |
" #print(sample, find_matching_normal(sample,list(set(d[\"Sample\"]))))\n", |
|
|
1539 |
" tumor = df_tumors.loc[df_tumors [\"Sample\"]== tumor_sample,:]\n", |
|
|
1540 |
" matching_normals = find_matching_normal(tumor_sample,normal_samples)\n", |
|
|
1541 |
" if len(matching_normals) >0:\n", |
|
|
1542 |
" n_segs = tumor.shape[0]\n", |
|
|
1543 |
" for normal_sample in matching_normals:\n", |
|
|
1544 |
" normal = df_normals.loc[df_normals[\"Sample\"]== normal_sample,:]\n", |
|
|
1545 |
" # thresholds for +1 and -1 copy in 75% of normal cell;\n", |
|
|
1546 |
" # this is to retain segments appeared due to slight tumor contamination\n", |
|
|
1547 |
" normal = filter_lowconf_segments(normal,0,0.46, -0.68 )\n", |
|
|
1548 |
" filtered_normals.append(normal)\n", |
|
|
1549 |
" tumor = remove_ovelapping_segments(tumor, normal,tumor_sample)\n", |
|
|
1550 |
" #if n_segs > tumor.shape[0]:\n", |
|
|
1551 |
" # print(n_segs - tumor.shape[0],\"segments removed in sample\",tumor_sample,\n", |
|
|
1552 |
" # tumor.shape[0],\"remained\",file= sys.stderr)\n", |
|
|
1553 |
" tumor = filter_lowconf_segments(tumor,num_marker_thr,pos_seg_mean_thr, neg_seg_mean_thr )\n", |
|
|
1554 |
" if tumor.shape[0] == 0:\n", |
|
|
1555 |
" tumors_without_somatic_CNA.append(tumor_sample)\n", |
|
|
1556 |
" else:\n", |
|
|
1557 |
" tumors_germline_removed.append(tumor)\n", |
|
|
1558 |
" else:\n", |
|
|
1559 |
" tumor = filter_lowconf_segments(tumor,num_marker_thr,pos_seg_mean_thr, neg_seg_mean_thr )\n", |
|
|
1560 |
" if tumor.shape[0] == 0:\n", |
|
|
1561 |
" tumors_without_somatic_CNA.append(tumor_sample)\n", |
|
|
1562 |
" else:\n", |
|
|
1563 |
" tumors_without_matching_normal.append(tumor)\n", |
|
|
1564 |
"\n", |
|
|
1565 |
" print(\"\\ttumors without matched normal\",len(tumors_without_matching_normal),file= sys.stderr)\n", |
|
|
1566 |
" print(\"\\ttumors with at least one sCNA\",len(tumors_germline_removed),file= sys.stderr)\n", |
|
|
1567 |
" print(\"\\ttumors without any somatic CNA\",len(tumors_without_somatic_CNA),file= sys.stderr)\n", |
|
|
1568 |
" #dfs[cohort] = df\n", |
|
|
1569 |
" filtered_tumors = pd.concat(tumors_germline_removed+tumors_without_matching_normal)\n", |
|
|
1570 |
" dfs[cohort] = filtered_tumors\n", |
|
|
1571 |
" filtered_normals = pd.concat(filtered_normals)\n", |
|
|
1572 |
" dfs_normals[cohort] = filtered_normals\n", |
|
|
1573 |
" tumors_without_CNA[cohort] = tumors_without_somatic_CNA\n", |
|
|
1574 |
" print(\"after filtering\")\n", |
|
|
1575 |
" print(cohort,\"samples:\",len(set(filtered_tumors[\"Sample\"].values)),\n", |
|
|
1576 |
" \"Segments per sample on avg.:\",float(filtered_tumors.shape[0])/len(set(filtered_tumors[\"Sample\"].values)))\n", |
|
|
1577 |
" \n", |
|
|
1578 |
" " |
|
|
1579 |
] |
|
|
1580 |
}, |
|
|
1581 |
{ |
|
|
1582 |
"cell_type": "code", |
|
|
1583 |
"execution_count": null, |
|
|
1584 |
"metadata": {}, |
|
|
1585 |
"outputs": [], |
|
|
1586 |
"source": [] |
|
|
1587 |
}, |
|
|
1588 |
{ |
|
|
1589 |
"cell_type": "markdown", |
|
|
1590 |
"metadata": {}, |
|
|
1591 |
"source": [ |
|
|
1592 |
"### Aggregating to gene-level\n", |
|
|
1593 |
"\n", |
|
|
1594 |
"Gene annotation must be:\n", |
|
|
1595 |
" - with Entrez gene IDs \n", |
|
|
1596 |
" - in hg19 coordinates\n", |
|
|
1597 |
" - with columns \"chrom\",\"start\",\"stop\",\"gene\" (this is foru-column bed format)\n", |
|
|
1598 |
" \n", |
|
|
1599 |
"wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.3/GFF/ref_GRCh37.p5_top_level.gff3.gz\n", |
|
|
1600 |
"\n", |
|
|
1601 |
"echo -e \"chrom\\tstart\\tstop\\tgene\\tname\" > ef_GRCh37.p5_top_level.gff3.bed;\n", |
|
|
1602 |
"zcat ref_GRCh37.p5_top_level.gff3.gz | awk '$3==\"gene\"' | cut -f 1,4,5,9| sed -e 's/;/\\t/g'| cut -f 1-3,5,6 | grep GeneID | sed -re 's/(Dbxref=GeneID:[0-9]*),.*/\\1/' | sed -e 's/Name=//' -e 's/Dbxref=GeneID://' | awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$5\"\\t\"$4}' >> \n", |
|
|
1603 |
"ref_GRCh37.p5_top_level.gff3.bed\n" |
|
|
1604 |
] |
|
|
1605 |
}, |
|
|
1606 |
{ |
|
|
1607 |
"cell_type": "code", |
|
|
1608 |
"execution_count": 15, |
|
|
1609 |
"metadata": {}, |
|
|
1610 |
"outputs": [], |
|
|
1611 |
"source": [ |
|
|
1612 |
"rename_chroms = {\"NC_000001.10\":1,\"NC_000002.11\":2,\"NC_000003.11\":3,\"NC_000004.11\":4,\n", |
|
|
1613 |
" \"NC_000005.9\":5,\"NC_000006.11\":6,\"NC_000007.13\":7,\"NC_000008.10\":8,\n", |
|
|
1614 |
" \"NC_000009.11\":9,\"NC_000010.10\":10,\"NC_000011.9\":11,\"NC_000012.11\":12,\"NC_000013.10\":13,\n", |
|
|
1615 |
" \"NC_000014.8\":14,\"NC_000015.9\":15,\"NC_000016.9\":16,\"NC_000017.10\":17,\n", |
|
|
1616 |
" \"NC_000018.9\":18,\"NC_000019.9\":19,\"NC_000020.10\":20,\"NC_000021.8\":21,\n", |
|
|
1617 |
" \"NC_000022.10\":22,\"NC_000023.10\":23,\"NC_000024.9\":24}" |
|
|
1618 |
] |
|
|
1619 |
}, |
|
|
1620 |
{ |
|
|
1621 |
"cell_type": "code", |
|
|
1622 |
"execution_count": 16, |
|
|
1623 |
"metadata": {}, |
|
|
1624 |
"outputs": [ |
|
|
1625 |
{ |
|
|
1626 |
"name": "stdout", |
|
|
1627 |
"output_type": "stream", |
|
|
1628 |
"text": [ |
|
|
1629 |
"(36019, 5)\n" |
|
|
1630 |
] |
|
|
1631 |
}, |
|
|
1632 |
{ |
|
|
1633 |
"data": { |
|
|
1634 |
"text/html": [ |
|
|
1635 |
"<div>\n", |
|
|
1636 |
"<style scoped>\n", |
|
|
1637 |
" .dataframe tbody tr th:only-of-type {\n", |
|
|
1638 |
" vertical-align: middle;\n", |
|
|
1639 |
" }\n", |
|
|
1640 |
"\n", |
|
|
1641 |
" .dataframe tbody tr th {\n", |
|
|
1642 |
" vertical-align: top;\n", |
|
|
1643 |
" }\n", |
|
|
1644 |
"\n", |
|
|
1645 |
" .dataframe thead th {\n", |
|
|
1646 |
" text-align: right;\n", |
|
|
1647 |
" }\n", |
|
|
1648 |
"</style>\n", |
|
|
1649 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
1650 |
" <thead>\n", |
|
|
1651 |
" <tr style=\"text-align: right;\">\n", |
|
|
1652 |
" <th></th>\n", |
|
|
1653 |
" <th>chrom</th>\n", |
|
|
1654 |
" <th>start</th>\n", |
|
|
1655 |
" <th>stop</th>\n", |
|
|
1656 |
" <th>gene</th>\n", |
|
|
1657 |
" <th>name</th>\n", |
|
|
1658 |
" </tr>\n", |
|
|
1659 |
" </thead>\n", |
|
|
1660 |
" <tbody>\n", |
|
|
1661 |
" <tr>\n", |
|
|
1662 |
" <th>0</th>\n", |
|
|
1663 |
" <td>1</td>\n", |
|
|
1664 |
" <td>10954</td>\n", |
|
|
1665 |
" <td>11507</td>\n", |
|
|
1666 |
" <td>100506145</td>\n", |
|
|
1667 |
" <td>LOC100506145</td>\n", |
|
|
1668 |
" </tr>\n", |
|
|
1669 |
" <tr>\n", |
|
|
1670 |
" <th>1</th>\n", |
|
|
1671 |
" <td>1</td>\n", |
|
|
1672 |
" <td>12190</td>\n", |
|
|
1673 |
" <td>13639</td>\n", |
|
|
1674 |
" <td>100652771</td>\n", |
|
|
1675 |
" <td>LOC100652771</td>\n", |
|
|
1676 |
" </tr>\n", |
|
|
1677 |
" <tr>\n", |
|
|
1678 |
" <th>2</th>\n", |
|
|
1679 |
" <td>1</td>\n", |
|
|
1680 |
" <td>14362</td>\n", |
|
|
1681 |
" <td>29370</td>\n", |
|
|
1682 |
" <td>653635</td>\n", |
|
|
1683 |
" <td>WASH7P</td>\n", |
|
|
1684 |
" </tr>\n", |
|
|
1685 |
" <tr>\n", |
|
|
1686 |
" <th>3</th>\n", |
|
|
1687 |
" <td>1</td>\n", |
|
|
1688 |
" <td>30366</td>\n", |
|
|
1689 |
" <td>30503</td>\n", |
|
|
1690 |
" <td>100302278</td>\n", |
|
|
1691 |
" <td>MIR1302-2</td>\n", |
|
|
1692 |
" </tr>\n", |
|
|
1693 |
" </tbody>\n", |
|
|
1694 |
"</table>\n", |
|
|
1695 |
"</div>" |
|
|
1696 |
], |
|
|
1697 |
"text/plain": [ |
|
|
1698 |
" chrom start stop gene name\n", |
|
|
1699 |
"0 1 10954 11507 100506145 LOC100506145\n", |
|
|
1700 |
"1 1 12190 13639 100652771 LOC100652771\n", |
|
|
1701 |
"2 1 14362 29370 653635 WASH7P\n", |
|
|
1702 |
"3 1 30366 30503 100302278 MIR1302-2" |
|
|
1703 |
] |
|
|
1704 |
}, |
|
|
1705 |
"execution_count": 16, |
|
|
1706 |
"metadata": {}, |
|
|
1707 |
"output_type": "execute_result" |
|
|
1708 |
} |
|
|
1709 |
], |
|
|
1710 |
"source": [ |
|
|
1711 |
"gene_intervals = pd.read_csv(gene_coords_file, sep = \"\\t\")\n", |
|
|
1712 |
"gene_intervals = gene_intervals.loc[gene_intervals[\"chrom\"].isin(rename_chroms.keys()),:]\n", |
|
|
1713 |
"gene_intervals[\"chrom\"] = gene_intervals[\"chrom\"].apply(lambda x : rename_chroms[x])\n", |
|
|
1714 |
"#print(\"chromosomes:\",list(set(gene_intervals[\"chrom\"].values)))\n", |
|
|
1715 |
"gene_intervals = gene_intervals.sort_values(by=[\"chrom\",\"start\",\"stop\"],ascending=True)\n", |
|
|
1716 |
"gene_intervals.to_csv(\"/home/olya/SFU/Hossein/v1/ref_GRCh37.p5_top_level.gff3.chroms_renamed.bed\",sep = \"\\t\",index=False)\n", |
|
|
1717 |
"print(gene_intervals.shape)\n", |
|
|
1718 |
"gene_intervals.head(4)" |
|
|
1719 |
] |
|
|
1720 |
}, |
|
|
1721 |
{ |
|
|
1722 |
"cell_type": "code", |
|
|
1723 |
"execution_count": 17, |
|
|
1724 |
"metadata": {}, |
|
|
1725 |
"outputs": [], |
|
|
1726 |
"source": [ |
|
|
1727 |
"gene_intervals_bed = pbt.BedTool.from_dataframe(gene_intervals[[\"chrom\",\"start\",\"stop\",\"gene\"]])\n", |
|
|
1728 |
"# prepare copy-neutral table\n", |
|
|
1729 |
"cnv_baseline = gene_intervals.copy()\n", |
|
|
1730 |
"cnv_baseline[\"Segment_Mean\"] = [0]*cnv_baseline.shape[0]\n", |
|
|
1731 |
"cnv_baseline = cnv_baseline[[\"gene\",\"Segment_Mean\"]]\n", |
|
|
1732 |
"cnv_baseline.set_index(\"gene\",inplace=True,drop=True)\n", |
|
|
1733 |
"cnv_baseline.sort_index(inplace=True)\n", |
|
|
1734 |
"sorted_index = list(cnv_baseline.index.values)" |
|
|
1735 |
] |
|
|
1736 |
}, |
|
|
1737 |
{ |
|
|
1738 |
"cell_type": "code", |
|
|
1739 |
"execution_count": 20, |
|
|
1740 |
"metadata": { |
|
|
1741 |
"scrolled": false |
|
|
1742 |
}, |
|
|
1743 |
"outputs": [ |
|
|
1744 |
{ |
|
|
1745 |
"name": "stderr", |
|
|
1746 |
"output_type": "stream", |
|
|
1747 |
"text": [ |
|
|
1748 |
"ESCA\n" |
|
|
1749 |
] |
|
|
1750 |
}, |
|
|
1751 |
{ |
|
|
1752 |
"name": "stdout", |
|
|
1753 |
"output_type": "stream", |
|
|
1754 |
"text": [ |
|
|
1755 |
"... 100 processed.\n", |
|
|
1756 |
"ESCA (36019, 185)\n" |
|
|
1757 |
] |
|
|
1758 |
}, |
|
|
1759 |
{ |
|
|
1760 |
"name": "stderr", |
|
|
1761 |
"output_type": "stream", |
|
|
1762 |
"text": [ |
|
|
1763 |
"DLBC\n", |
|
|
1764 |
"TCGA-G8-6914-14A-01D-2209-01 has no genes with altered CN\n" |
|
|
1765 |
] |
|
|
1766 |
}, |
|
|
1767 |
{ |
|
|
1768 |
"name": "stdout", |
|
|
1769 |
"output_type": "stream", |
|
|
1770 |
"text": [ |
|
|
1771 |
"DLBC (36019, 52)\n" |
|
|
1772 |
] |
|
|
1773 |
}, |
|
|
1774 |
{ |
|
|
1775 |
"name": "stderr", |
|
|
1776 |
"output_type": "stream", |
|
|
1777 |
"text": [ |
|
|
1778 |
"READ\n" |
|
|
1779 |
] |
|
|
1780 |
}, |
|
|
1781 |
{ |
|
|
1782 |
"name": "stdout", |
|
|
1783 |
"output_type": "stream", |
|
|
1784 |
"text": [ |
|
|
1785 |
"... 100 processed.\n", |
|
|
1786 |
"READ (36019, 166)\n" |
|
|
1787 |
] |
|
|
1788 |
}, |
|
|
1789 |
{ |
|
|
1790 |
"name": "stderr", |
|
|
1791 |
"output_type": "stream", |
|
|
1792 |
"text": [ |
|
|
1793 |
"GBM\n", |
|
|
1794 |
"TCGA-06-0165-01A-01D-0236-01 has no genes with altered CN\n" |
|
|
1795 |
] |
|
|
1796 |
}, |
|
|
1797 |
{ |
|
|
1798 |
"name": "stdout", |
|
|
1799 |
"output_type": "stream", |
|
|
1800 |
"text": [ |
|
|
1801 |
"... 100 processed.\n", |
|
|
1802 |
"... 200 processed.\n" |
|
|
1803 |
] |
|
|
1804 |
}, |
|
|
1805 |
{ |
|
|
1806 |
"name": "stderr", |
|
|
1807 |
"output_type": "stream", |
|
|
1808 |
"text": [ |
|
|
1809 |
"TCGA-06-0119-01A-08D-0214-01 has no genes with altered CN\n" |
|
|
1810 |
] |
|
|
1811 |
}, |
|
|
1812 |
{ |
|
|
1813 |
"name": "stdout", |
|
|
1814 |
"output_type": "stream", |
|
|
1815 |
"text": [ |
|
|
1816 |
"... 300 processed.\n", |
|
|
1817 |
"... 400 processed.\n", |
|
|
1818 |
"... 500 processed.\n" |
|
|
1819 |
] |
|
|
1820 |
}, |
|
|
1821 |
{ |
|
|
1822 |
"name": "stderr", |
|
|
1823 |
"output_type": "stream", |
|
|
1824 |
"text": [ |
|
|
1825 |
"TCGA-06-5410-01A-01D-1694-01 has no genes with altered CN\n" |
|
|
1826 |
] |
|
|
1827 |
}, |
|
|
1828 |
{ |
|
|
1829 |
"name": "stdout", |
|
|
1830 |
"output_type": "stream", |
|
|
1831 |
"text": [ |
|
|
1832 |
"GBM (36019, 590)\n" |
|
|
1833 |
] |
|
|
1834 |
}, |
|
|
1835 |
{ |
|
|
1836 |
"name": "stderr", |
|
|
1837 |
"output_type": "stream", |
|
|
1838 |
"text": [ |
|
|
1839 |
"STES\n", |
|
|
1840 |
"TCGA-MX-A5UG-01A-21D-A31K-01 has no genes with altered CN\n", |
|
|
1841 |
"TCGA-RD-A8NB-01A-12D-A396-01 has no genes with altered CN\n" |
|
|
1842 |
] |
|
|
1843 |
}, |
|
|
1844 |
{ |
|
|
1845 |
"name": "stdout", |
|
|
1846 |
"output_type": "stream", |
|
|
1847 |
"text": [ |
|
|
1848 |
"... 100 processed.\n" |
|
|
1849 |
] |
|
|
1850 |
}, |
|
|
1851 |
{ |
|
|
1852 |
"name": "stderr", |
|
|
1853 |
"output_type": "stream", |
|
|
1854 |
"text": [ |
|
|
1855 |
"TCGA-BR-7957-01A-11D-2200-01 has no genes with altered CN\n" |
|
|
1856 |
] |
|
|
1857 |
}, |
|
|
1858 |
{ |
|
|
1859 |
"name": "stdout", |
|
|
1860 |
"output_type": "stream", |
|
|
1861 |
"text": [ |
|
|
1862 |
"... 200 processed.\n", |
|
|
1863 |
"... 300 processed.\n" |
|
|
1864 |
] |
|
|
1865 |
}, |
|
|
1866 |
{ |
|
|
1867 |
"name": "stderr", |
|
|
1868 |
"output_type": "stream", |
|
|
1869 |
"text": [ |
|
|
1870 |
"TCGA-BR-6563-01A-13D-2052-01 has no genes with altered CN\n", |
|
|
1871 |
"TCGA-D7-6522-01A-11D-1799-01 has no genes with altered CN\n", |
|
|
1872 |
"TCGA-BR-7196-01A-11D-2052-01 has no genes with altered CN\n" |
|
|
1873 |
] |
|
|
1874 |
}, |
|
|
1875 |
{ |
|
|
1876 |
"name": "stdout", |
|
|
1877 |
"output_type": "stream", |
|
|
1878 |
"text": [ |
|
|
1879 |
"... 400 processed.\n" |
|
|
1880 |
] |
|
|
1881 |
}, |
|
|
1882 |
{ |
|
|
1883 |
"name": "stderr", |
|
|
1884 |
"output_type": "stream", |
|
|
1885 |
"text": [ |
|
|
1886 |
"TCGA-D7-A6ET-01A-32D-A32M-01 has no genes with altered CN\n" |
|
|
1887 |
] |
|
|
1888 |
}, |
|
|
1889 |
{ |
|
|
1890 |
"name": "stdout", |
|
|
1891 |
"output_type": "stream", |
|
|
1892 |
"text": [ |
|
|
1893 |
"... 500 processed.\n" |
|
|
1894 |
] |
|
|
1895 |
}, |
|
|
1896 |
{ |
|
|
1897 |
"name": "stderr", |
|
|
1898 |
"output_type": "stream", |
|
|
1899 |
"text": [ |
|
|
1900 |
"TCGA-HU-A4GJ-01A-11D-A253-01 has no genes with altered CN\n" |
|
|
1901 |
] |
|
|
1902 |
}, |
|
|
1903 |
{ |
|
|
1904 |
"name": "stdout", |
|
|
1905 |
"output_type": "stream", |
|
|
1906 |
"text": [ |
|
|
1907 |
"... 600 processed.\n", |
|
|
1908 |
"STES (36019, 627)\n" |
|
|
1909 |
] |
|
|
1910 |
}, |
|
|
1911 |
{ |
|
|
1912 |
"name": "stderr", |
|
|
1913 |
"output_type": "stream", |
|
|
1914 |
"text": [ |
|
|
1915 |
"BLCA\n", |
|
|
1916 |
"TCGA-YC-A8S6-01A-31D-A38F-01 has no genes with altered CN\n" |
|
|
1917 |
] |
|
|
1918 |
}, |
|
|
1919 |
{ |
|
|
1920 |
"name": "stdout", |
|
|
1921 |
"output_type": "stream", |
|
|
1922 |
"text": [ |
|
|
1923 |
"... 100 processed.\n" |
|
|
1924 |
] |
|
|
1925 |
}, |
|
|
1926 |
{ |
|
|
1927 |
"name": "stderr", |
|
|
1928 |
"output_type": "stream", |
|
|
1929 |
"text": [ |
|
|
1930 |
"TCGA-DK-A3WY-01A-11D-A22Y-01 has no genes with altered CN\n", |
|
|
1931 |
"TCGA-XF-A9SL-01A-11D-A390-01 has no genes with altered CN\n" |
|
|
1932 |
] |
|
|
1933 |
}, |
|
|
1934 |
{ |
|
|
1935 |
"name": "stdout", |
|
|
1936 |
"output_type": "stream", |
|
|
1937 |
"text": [ |
|
|
1938 |
"... 200 processed.\n" |
|
|
1939 |
] |
|
|
1940 |
}, |
|
|
1941 |
{ |
|
|
1942 |
"name": "stderr", |
|
|
1943 |
"output_type": "stream", |
|
|
1944 |
"text": [ |
|
|
1945 |
"TCGA-E7-A7XN-01A-11D-A34T-01 has no genes with altered CN\n" |
|
|
1946 |
] |
|
|
1947 |
}, |
|
|
1948 |
{ |
|
|
1949 |
"name": "stdout", |
|
|
1950 |
"output_type": "stream", |
|
|
1951 |
"text": [ |
|
|
1952 |
"... 300 processed.\n", |
|
|
1953 |
"... 400 processed.\n", |
|
|
1954 |
"BLCA (36019, 414)\n" |
|
|
1955 |
] |
|
|
1956 |
}, |
|
|
1957 |
{ |
|
|
1958 |
"name": "stderr", |
|
|
1959 |
"output_type": "stream", |
|
|
1960 |
"text": [ |
|
|
1961 |
"UCEC\n", |
|
|
1962 |
"TCGA-D1-A16Y-01A-31D-A12G-01 has no genes with altered CN\n", |
|
|
1963 |
"TCGA-BK-A6W4-01A-12D-A34P-01 has no genes with altered CN\n", |
|
|
1964 |
"TCGA-BS-A0V7-01A-21D-A120-01 has no genes with altered CN\n", |
|
|
1965 |
"TCGA-B5-A11Y-01A-21D-A10L-01 has no genes with altered CN\n", |
|
|
1966 |
"TCGA-D1-A17F-01A-11D-A12G-01 has no genes with altered CN\n" |
|
|
1967 |
] |
|
|
1968 |
}, |
|
|
1969 |
{ |
|
|
1970 |
"name": "stdout", |
|
|
1971 |
"output_type": "stream", |
|
|
1972 |
"text": [ |
|
|
1973 |
"... 100 processed.\n" |
|
|
1974 |
] |
|
|
1975 |
}, |
|
|
1976 |
{ |
|
|
1977 |
"name": "stderr", |
|
|
1978 |
"output_type": "stream", |
|
|
1979 |
"text": [ |
|
|
1980 |
"TCGA-AX-A062-01A-11D-A00X-01 has no genes with altered CN\n", |
|
|
1981 |
"TCGA-D1-A16D-01A-11D-A12G-01 has no genes with altered CN\n", |
|
|
1982 |
"TCGA-BG-A0VZ-01A-11D-A107-01 has no genes with altered CN\n" |
|
|
1983 |
] |
|
|
1984 |
}, |
|
|
1985 |
{ |
|
|
1986 |
"name": "stdout", |
|
|
1987 |
"output_type": "stream", |
|
|
1988 |
"text": [ |
|
|
1989 |
"... 200 processed.\n" |
|
|
1990 |
] |
|
|
1991 |
}, |
|
|
1992 |
{ |
|
|
1993 |
"name": "stderr", |
|
|
1994 |
"output_type": "stream", |
|
|
1995 |
"text": [ |
|
|
1996 |
"TCGA-AJ-A2QL-01A-11D-A18N-01 has no genes with altered CN\n", |
|
|
1997 |
"TCGA-BS-A0UA-01A-11D-A120-01 has no genes with altered CN\n", |
|
|
1998 |
"TCGA-B5-A11U-01A-11D-A120-01 has no genes with altered CN\n" |
|
|
1999 |
] |
|
|
2000 |
}, |
|
|
2001 |
{ |
|
|
2002 |
"name": "stdout", |
|
|
2003 |
"output_type": "stream", |
|
|
2004 |
"text": [ |
|
|
2005 |
"... 300 processed.\n" |
|
|
2006 |
] |
|
|
2007 |
}, |
|
|
2008 |
{ |
|
|
2009 |
"name": "stderr", |
|
|
2010 |
"output_type": "stream", |
|
|
2011 |
"text": [ |
|
|
2012 |
"TCGA-EO-A3AU-01A-21D-A19X-01 has no genes with altered CN\n", |
|
|
2013 |
"TCGA-QF-A5YS-01A-11D-A31T-01 has no genes with altered CN\n", |
|
|
2014 |
"TCGA-D1-A0ZV-01A-11D-A10L-01 has no genes with altered CN\n" |
|
|
2015 |
] |
|
|
2016 |
}, |
|
|
2017 |
{ |
|
|
2018 |
"name": "stdout", |
|
|
2019 |
"output_type": "stream", |
|
|
2020 |
"text": [ |
|
|
2021 |
"... 400 processed.\n" |
|
|
2022 |
] |
|
|
2023 |
}, |
|
|
2024 |
{ |
|
|
2025 |
"name": "stderr", |
|
|
2026 |
"output_type": "stream", |
|
|
2027 |
"text": [ |
|
|
2028 |
"TCGA-QS-A5YR-01A-31D-A31T-01 has no genes with altered CN\n", |
|
|
2029 |
"TCGA-DI-A1BU-01A-11D-A134-01 has no genes with altered CN\n", |
|
|
2030 |
"TCGA-AP-A0LG-01A-11D-A042-01 has no genes with altered CN\n" |
|
|
2031 |
] |
|
|
2032 |
}, |
|
|
2033 |
{ |
|
|
2034 |
"name": "stdout", |
|
|
2035 |
"output_type": "stream", |
|
|
2036 |
"text": [ |
|
|
2037 |
"... 500 processed.\n" |
|
|
2038 |
] |
|
|
2039 |
}, |
|
|
2040 |
{ |
|
|
2041 |
"name": "stderr", |
|
|
2042 |
"output_type": "stream", |
|
|
2043 |
"text": [ |
|
|
2044 |
"TCGA-D1-A0ZS-01A-11D-A120-01 has no genes with altered CN\n" |
|
|
2045 |
] |
|
|
2046 |
}, |
|
|
2047 |
{ |
|
|
2048 |
"name": "stdout", |
|
|
2049 |
"output_type": "stream", |
|
|
2050 |
"text": [ |
|
|
2051 |
"UCEC (36019, 540)\n" |
|
|
2052 |
] |
|
|
2053 |
}, |
|
|
2054 |
{ |
|
|
2055 |
"name": "stderr", |
|
|
2056 |
"output_type": "stream", |
|
|
2057 |
"text": [ |
|
|
2058 |
"PCPG\n", |
|
|
2059 |
"TCGA-RW-A7CZ-01A-11D-A35C-01 has no genes with altered CN\n" |
|
|
2060 |
] |
|
|
2061 |
}, |
|
|
2062 |
{ |
|
|
2063 |
"name": "stdout", |
|
|
2064 |
"output_type": "stream", |
|
|
2065 |
"text": [ |
|
|
2066 |
"... 100 processed.\n" |
|
|
2067 |
] |
|
|
2068 |
}, |
|
|
2069 |
{ |
|
|
2070 |
"name": "stderr", |
|
|
2071 |
"output_type": "stream", |
|
|
2072 |
"text": [ |
|
|
2073 |
"TCGA-WB-A817-01A-11D-A35H-01 has no genes with altered CN\n" |
|
|
2074 |
] |
|
|
2075 |
}, |
|
|
2076 |
{ |
|
|
2077 |
"name": "stdout", |
|
|
2078 |
"output_type": "stream", |
|
|
2079 |
"text": [ |
|
|
2080 |
"PCPG (36019, 168)\n" |
|
|
2081 |
] |
|
|
2082 |
}, |
|
|
2083 |
{ |
|
|
2084 |
"name": "stderr", |
|
|
2085 |
"output_type": "stream", |
|
|
2086 |
"text": [ |
|
|
2087 |
"STAD\n", |
|
|
2088 |
"TCGA-MX-A5UG-01A-21D-A31K-01 has no genes with altered CN\n", |
|
|
2089 |
"TCGA-RD-A8NB-01A-12D-A396-01 has no genes with altered CN\n" |
|
|
2090 |
] |
|
|
2091 |
}, |
|
|
2092 |
{ |
|
|
2093 |
"name": "stdout", |
|
|
2094 |
"output_type": "stream", |
|
|
2095 |
"text": [ |
|
|
2096 |
"... 100 processed.\n" |
|
|
2097 |
] |
|
|
2098 |
}, |
|
|
2099 |
{ |
|
|
2100 |
"name": "stderr", |
|
|
2101 |
"output_type": "stream", |
|
|
2102 |
"text": [ |
|
|
2103 |
"TCGA-BR-7957-01A-11D-2200-01 has no genes with altered CN\n" |
|
|
2104 |
] |
|
|
2105 |
}, |
|
|
2106 |
{ |
|
|
2107 |
"name": "stdout", |
|
|
2108 |
"output_type": "stream", |
|
|
2109 |
"text": [ |
|
|
2110 |
"... 200 processed.\n" |
|
|
2111 |
] |
|
|
2112 |
}, |
|
|
2113 |
{ |
|
|
2114 |
"name": "stderr", |
|
|
2115 |
"output_type": "stream", |
|
|
2116 |
"text": [ |
|
|
2117 |
"TCGA-BR-6563-01A-13D-2052-01 has no genes with altered CN\n", |
|
|
2118 |
"TCGA-D7-6522-01A-11D-1799-01 has no genes with altered CN\n", |
|
|
2119 |
"TCGA-BR-7196-01A-11D-2052-01 has no genes with altered CN\n" |
|
|
2120 |
] |
|
|
2121 |
}, |
|
|
2122 |
{ |
|
|
2123 |
"name": "stdout", |
|
|
2124 |
"output_type": "stream", |
|
|
2125 |
"text": [ |
|
|
2126 |
"... 300 processed.\n" |
|
|
2127 |
] |
|
|
2128 |
}, |
|
|
2129 |
{ |
|
|
2130 |
"name": "stderr", |
|
|
2131 |
"output_type": "stream", |
|
|
2132 |
"text": [ |
|
|
2133 |
"TCGA-D7-A6ET-01A-32D-A32M-01 has no genes with altered CN\n", |
|
|
2134 |
"TCGA-HU-A4GJ-01A-11D-A253-01 has no genes with altered CN\n" |
|
|
2135 |
] |
|
|
2136 |
}, |
|
|
2137 |
{ |
|
|
2138 |
"name": "stdout", |
|
|
2139 |
"output_type": "stream", |
|
|
2140 |
"text": [ |
|
|
2141 |
"... 400 processed.\n", |
|
|
2142 |
"STAD (36019, 442)\n" |
|
|
2143 |
] |
|
|
2144 |
}, |
|
|
2145 |
{ |
|
|
2146 |
"name": "stderr", |
|
|
2147 |
"output_type": "stream", |
|
|
2148 |
"text": [ |
|
|
2149 |
"CESC\n" |
|
|
2150 |
] |
|
|
2151 |
}, |
|
|
2152 |
{ |
|
|
2153 |
"name": "stdout", |
|
|
2154 |
"output_type": "stream", |
|
|
2155 |
"text": [ |
|
|
2156 |
"... 100 processed.\n", |
|
|
2157 |
"... 200 processed.\n", |
|
|
2158 |
"CESC (36019, 297)\n" |
|
|
2159 |
] |
|
|
2160 |
}, |
|
|
2161 |
{ |
|
|
2162 |
"name": "stderr", |
|
|
2163 |
"output_type": "stream", |
|
|
2164 |
"text": [ |
|
|
2165 |
"UCS\n" |
|
|
2166 |
] |
|
|
2167 |
}, |
|
|
2168 |
{ |
|
|
2169 |
"name": "stdout", |
|
|
2170 |
"output_type": "stream", |
|
|
2171 |
"text": [ |
|
|
2172 |
"UCS (36019, 56)\n" |
|
|
2173 |
] |
|
|
2174 |
}, |
|
|
2175 |
{ |
|
|
2176 |
"name": "stderr", |
|
|
2177 |
"output_type": "stream", |
|
|
2178 |
"text": [ |
|
|
2179 |
"TGCT\n", |
|
|
2180 |
"TCGA-YU-A90S-01A-11D-A434-01 has no genes with altered CN\n" |
|
|
2181 |
] |
|
|
2182 |
}, |
|
|
2183 |
{ |
|
|
2184 |
"name": "stdout", |
|
|
2185 |
"output_type": "stream", |
|
|
2186 |
"text": [ |
|
|
2187 |
"... 100 processed.\n", |
|
|
2188 |
"TGCT (36019, 156)\n" |
|
|
2189 |
] |
|
|
2190 |
}, |
|
|
2191 |
{ |
|
|
2192 |
"name": "stderr", |
|
|
2193 |
"output_type": "stream", |
|
|
2194 |
"text": [ |
|
|
2195 |
"THCA\n", |
|
|
2196 |
"TCGA-EL-A4JZ-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2197 |
"TCGA-DJ-A13X-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2198 |
"TCGA-EL-A3ZT-01A-12D-A23L-01 has no genes with altered CN\n", |
|
|
2199 |
"TCGA-DE-A0XZ-01A-11D-A17S-01 has no genes with altered CN\n", |
|
|
2200 |
"TCGA-DJ-A2PP-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2201 |
"TCGA-KS-A4I5-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2202 |
"TCGA-DJ-A2PS-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2203 |
"TCGA-EL-A3GW-01A-11D-A201-01 has no genes with altered CN\n", |
|
|
2204 |
"TCGA-BJ-A0ZG-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2205 |
"TCGA-J8-A3O2-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2206 |
"TCGA-FY-A3RA-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2207 |
"TCGA-CE-A483-01A-11D-A23T-01 has no genes with altered CN\n", |
|
|
2208 |
"TCGA-EM-A1CW-01A-21D-A13V-01 has no genes with altered CN\n", |
|
|
2209 |
"TCGA-DJ-A4V4-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2210 |
"TCGA-E3-A3E1-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2211 |
"TCGA-ET-A2MZ-01A-12D-A19I-01 has no genes with altered CN\n", |
|
|
2212 |
"TCGA-E8-A414-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2213 |
"TCGA-EL-A3T6-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2214 |
"TCGA-DJ-A4V5-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2215 |
"TCGA-DJ-A3UY-01A-21D-A22C-01 has no genes with altered CN\n", |
|
|
2216 |
"TCGA-EL-A3D4-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2217 |
"TCGA-FY-A76V-01A-11D-A396-01 has no genes with altered CN\n", |
|
|
2218 |
"TCGA-FY-A4B3-01A-11D-A23T-01 has no genes with altered CN\n", |
|
|
2219 |
"TCGA-DJ-A3UO-01A-11D-A22C-01 has no genes with altered CN\n", |
|
|
2220 |
"TCGA-EL-A4K7-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2221 |
"TCGA-DJ-A1QI-01A-11D-A14V-01 has no genes with altered CN\n", |
|
|
2222 |
"TCGA-EL-A3N2-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2223 |
"TCGA-E3-A3E5-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2224 |
"TCGA-EM-A1YD-01A-11D-A14V-01 has no genes with altered CN\n", |
|
|
2225 |
"TCGA-GE-A2C6-01A-11D-A16M-01 has no genes with altered CN\n", |
|
|
2226 |
"TCGA-DJ-A2Q5-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2227 |
"TCGA-ET-A3DP-01A-11D-A219-01 has no genes with altered CN\n", |
|
|
2228 |
"TCGA-DJ-A4UT-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2229 |
"TCGA-DJ-A2PT-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2230 |
"TCGA-DJ-A4V2-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2231 |
"TCGA-L6-A4ET-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2232 |
"TCGA-BJ-A0ZJ-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2233 |
"TCGA-DE-A4M9-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2234 |
"TCGA-EL-A4KD-01A-11D-A256-01 has no genes with altered CN\n" |
|
|
2235 |
] |
|
|
2236 |
}, |
|
|
2237 |
{ |
|
|
2238 |
"name": "stdout", |
|
|
2239 |
"output_type": "stream", |
|
|
2240 |
"text": [ |
|
|
2241 |
"... 100 processed.\n" |
|
|
2242 |
] |
|
|
2243 |
}, |
|
|
2244 |
{ |
|
|
2245 |
"name": "stderr", |
|
|
2246 |
"output_type": "stream", |
|
|
2247 |
"text": [ |
|
|
2248 |
"TCGA-QD-A8IV-01A-11D-A396-01 has no genes with altered CN\n", |
|
|
2249 |
"TCGA-ET-A3DV-01A-12D-A201-01 has no genes with altered CN\n", |
|
|
2250 |
"TCGA-EM-A22K-01A-11D-A17S-01 has no genes with altered CN\n", |
|
|
2251 |
"TCGA-DJ-A3VE-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2252 |
"TCGA-EL-A3D1-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2253 |
"TCGA-BJ-A2P4-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2254 |
"TCGA-CE-A3ME-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2255 |
"TCGA-E8-A417-01A-21D-A23L-01 has no genes with altered CN\n", |
|
|
2256 |
"TCGA-KS-A41I-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2257 |
"TCGA-FK-A3SB-01A-11D-A22C-01 has no genes with altered CN\n", |
|
|
2258 |
"TCGA-BJ-A28S-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2259 |
"TCGA-MK-A4N9-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2260 |
"TCGA-E8-A437-01A-12D-A23T-01 has no genes with altered CN\n", |
|
|
2261 |
"TCGA-EM-A3AP-01A-12D-A20A-01 has no genes with altered CN\n", |
|
|
2262 |
"TCGA-EL-A3TA-01A-12D-A22C-01 has no genes with altered CN\n", |
|
|
2263 |
"TCGA-IM-A41Z-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2264 |
"TCGA-EM-A2CQ-01A-11D-A17S-01 has no genes with altered CN\n", |
|
|
2265 |
"TCGA-EM-A3O7-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2266 |
"TCGA-FE-A3PC-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2267 |
"TCGA-DJ-A2PY-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2268 |
"TCGA-EM-A4FQ-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2269 |
"TCGA-EM-A3FO-01A-11D-A219-01 has no genes with altered CN\n", |
|
|
2270 |
"TCGA-BJ-A0Z9-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2271 |
"TCGA-EM-A3FK-01A-11D-A219-01 has no genes with altered CN\n" |
|
|
2272 |
] |
|
|
2273 |
}, |
|
|
2274 |
{ |
|
|
2275 |
"name": "stdout", |
|
|
2276 |
"output_type": "stream", |
|
|
2277 |
"text": [ |
|
|
2278 |
"... 200 processed.\n" |
|
|
2279 |
] |
|
|
2280 |
}, |
|
|
2281 |
{ |
|
|
2282 |
"name": "stderr", |
|
|
2283 |
"output_type": "stream", |
|
|
2284 |
"text": [ |
|
|
2285 |
"TCGA-ET-A3BU-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2286 |
"TCGA-BJ-A0Z5-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2287 |
"TCGA-EL-A3MY-01A-11D-A219-01 has no genes with altered CN\n", |
|
|
2288 |
"TCGA-ET-A39L-01A-12D-A19I-01 has no genes with altered CN\n", |
|
|
2289 |
"TCGA-E8-A415-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2290 |
"TCGA-ET-A40Q-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2291 |
"TCGA-KS-A4I7-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2292 |
"TCGA-MK-A4N7-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2293 |
"TCGA-L6-A4EQ-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2294 |
"TCGA-FY-A3TY-01A-11D-A22Y-01 has no genes with altered CN\n", |
|
|
2295 |
"TCGA-ET-A2N1-01A-11D-A18E-01 has no genes with altered CN\n", |
|
|
2296 |
"TCGA-DJ-A2PO-01A-21D-A19I-01 has no genes with altered CN\n", |
|
|
2297 |
"TCGA-J8-A3O2-06A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2298 |
"TCGA-CE-A485-01A-11D-A23T-01 has no genes with altered CN\n", |
|
|
2299 |
"TCGA-ET-A3BX-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2300 |
"TCGA-DJ-A3VK-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2301 |
"TCGA-DE-A4M8-01A-21D-A256-01 has no genes with altered CN\n", |
|
|
2302 |
"TCGA-ET-A40T-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2303 |
"TCGA-BJ-A18Z-01A-21D-A13V-01 has no genes with altered CN\n", |
|
|
2304 |
"TCGA-DJ-A3UT-01A-11D-A22C-01 has no genes with altered CN\n", |
|
|
2305 |
"TCGA-DJ-A2Q2-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2306 |
"TCGA-BJ-A18Y-01A-11D-A13V-01 has no genes with altered CN\n", |
|
|
2307 |
"TCGA-ET-A39T-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2308 |
"TCGA-EL-A3CL-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2309 |
"TCGA-DJ-A4V0-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2310 |
"TCGA-EL-A3H8-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2311 |
"TCGA-ET-A39J-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2312 |
"TCGA-FY-A3I4-01A-11D-A219-01 has no genes with altered CN\n", |
|
|
2313 |
"TCGA-EM-A2CU-01A-12D-A17S-01 has no genes with altered CN\n" |
|
|
2314 |
] |
|
|
2315 |
}, |
|
|
2316 |
{ |
|
|
2317 |
"name": "stdout", |
|
|
2318 |
"output_type": "stream", |
|
|
2319 |
"text": [ |
|
|
2320 |
"... 300 processed.\n" |
|
|
2321 |
] |
|
|
2322 |
}, |
|
|
2323 |
{ |
|
|
2324 |
"name": "stderr", |
|
|
2325 |
"output_type": "stream", |
|
|
2326 |
"text": [ |
|
|
2327 |
"TCGA-EM-A3FM-01A-11D-A219-01 has no genes with altered CN\n", |
|
|
2328 |
"TCGA-EM-A4FF-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2329 |
"TCGA-EL-A3GX-01A-11D-A201-01 has no genes with altered CN\n", |
|
|
2330 |
"TCGA-DJ-A3UN-01A-11D-A22C-01 has no genes with altered CN\n", |
|
|
2331 |
"TCGA-EM-A4FO-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2332 |
"TCGA-EL-A3TB-01A-11D-A22C-01 has no genes with altered CN\n", |
|
|
2333 |
"TCGA-ET-A25N-01A-11D-A16M-01 has no genes with altered CN\n", |
|
|
2334 |
"TCGA-ET-A39M-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2335 |
"TCGA-DE-A4MA-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2336 |
"TCGA-ET-A39O-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2337 |
"TCGA-DE-A0Y2-01A-11D-A10T-01 has no genes with altered CN\n", |
|
|
2338 |
"TCGA-FY-A3R8-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2339 |
"TCGA-EM-A3AL-01A-11D-A201-01 has no genes with altered CN\n", |
|
|
2340 |
"TCGA-EM-A2CN-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2341 |
"TCGA-FY-A3BL-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2342 |
"TCGA-EM-A1CS-01A-11D-A13V-01 has no genes with altered CN\n", |
|
|
2343 |
"TCGA-EL-A3D0-01A-12D-A201-01 has no genes with altered CN\n", |
|
|
2344 |
"TCGA-E3-A3DZ-01A-11D-A20A-01 has no genes with altered CN\n", |
|
|
2345 |
"TCGA-DJ-A1QF-01A-12D-A14V-01 has no genes with altered CN\n", |
|
|
2346 |
"TCGA-J8-A3YH-01A-11D-A22Y-01 has no genes with altered CN\n", |
|
|
2347 |
"TCGA-EL-A4K1-01A-11D-A256-01 has no genes with altered CN\n", |
|
|
2348 |
"TCGA-EM-A3O8-01A-11D-A21Y-01 has no genes with altered CN\n", |
|
|
2349 |
"TCGA-DJ-A3VJ-01A-11D-A23L-01 has no genes with altered CN\n", |
|
|
2350 |
"TCGA-BJ-A45D-01A-11D-A23T-01 has no genes with altered CN\n", |
|
|
2351 |
"TCGA-FY-A4B4-01A-11D-A23T-01 has no genes with altered CN\n", |
|
|
2352 |
"TCGA-EM-A1CU-01A-11D-A13V-01 has no genes with altered CN\n", |
|
|
2353 |
"TCGA-EL-A3CX-01A-11D-A19I-01 has no genes with altered CN\n", |
|
|
2354 |
"TCGA-ET-A25O-01A-11D-A16M-01 has no genes with altered CN\n", |
|
|
2355 |
"TCGA-E8-A433-01A-11D-A23L-01 has no genes with altered CN\n" |
|
|
2356 |
] |
|
|
2357 |
}, |
|
|
2358 |
{ |
|
|
2359 |
"name": "stdout", |
|
|
2360 |
"output_type": "stream", |
|
|
2361 |
"text": [ |
|
|
2362 |
"THCA (36019, 506)\n" |
|
|
2363 |
] |
|
|
2364 |
}, |
|
|
2365 |
{ |
|
|
2366 |
"name": "stderr", |
|
|
2367 |
"output_type": "stream", |
|
|
2368 |
"text": [ |
|
|
2369 |
"CHOL\n", |
|
|
2370 |
"TCGA-W5-AA2H-01A-31D-A416-01 has no genes with altered CN\n" |
|
|
2371 |
] |
|
|
2372 |
}, |
|
|
2373 |
{ |
|
|
2374 |
"name": "stdout", |
|
|
2375 |
"output_type": "stream", |
|
|
2376 |
"text": [ |
|
|
2377 |
"CHOL (36019, 36)\n" |
|
|
2378 |
] |
|
|
2379 |
}, |
|
|
2380 |
{ |
|
|
2381 |
"name": "stderr", |
|
|
2382 |
"output_type": "stream", |
|
|
2383 |
"text": [ |
|
|
2384 |
"HNSC\n" |
|
|
2385 |
] |
|
|
2386 |
}, |
|
|
2387 |
{ |
|
|
2388 |
"name": "stdout", |
|
|
2389 |
"output_type": "stream", |
|
|
2390 |
"text": [ |
|
|
2391 |
"... 100 processed.\n", |
|
|
2392 |
"... 200 processed.\n", |
|
|
2393 |
"... 300 processed.\n", |
|
|
2394 |
"... 400 processed.\n", |
|
|
2395 |
"... 500 processed.\n", |
|
|
2396 |
"HNSC (36019, 530)\n" |
|
|
2397 |
] |
|
|
2398 |
}, |
|
|
2399 |
{ |
|
|
2400 |
"name": "stderr", |
|
|
2401 |
"output_type": "stream", |
|
|
2402 |
"text": [ |
|
|
2403 |
"UVM\n" |
|
|
2404 |
] |
|
|
2405 |
}, |
|
|
2406 |
{ |
|
|
2407 |
"name": "stdout", |
|
|
2408 |
"output_type": "stream", |
|
|
2409 |
"text": [ |
|
|
2410 |
"UVM (36019, 80)\n" |
|
|
2411 |
] |
|
|
2412 |
}, |
|
|
2413 |
{ |
|
|
2414 |
"name": "stderr", |
|
|
2415 |
"output_type": "stream", |
|
|
2416 |
"text": [ |
|
|
2417 |
"SKCM\n", |
|
|
2418 |
"TCGA-ER-A19A-06A-21D-A191-01 has no genes with altered CN\n" |
|
|
2419 |
] |
|
|
2420 |
}, |
|
|
2421 |
{ |
|
|
2422 |
"name": "stdout", |
|
|
2423 |
"output_type": "stream", |
|
|
2424 |
"text": [ |
|
|
2425 |
"... 100 processed.\n", |
|
|
2426 |
"... 200 processed.\n", |
|
|
2427 |
"... 300 processed.\n", |
|
|
2428 |
"... 400 processed.\n" |
|
|
2429 |
] |
|
|
2430 |
}, |
|
|
2431 |
{ |
|
|
2432 |
"name": "stderr", |
|
|
2433 |
"output_type": "stream", |
|
|
2434 |
"text": [ |
|
|
2435 |
"TCGA-EB-A4OZ-01A-12D-A25P-01 has no genes with altered CN\n", |
|
|
2436 |
"TCGA-EE-A2GK-06A-11D-A194-01 has no genes with altered CN\n" |
|
|
2437 |
] |
|
|
2438 |
}, |
|
|
2439 |
{ |
|
|
2440 |
"name": "stdout", |
|
|
2441 |
"output_type": "stream", |
|
|
2442 |
"text": [ |
|
|
2443 |
"SKCM (36019, 472)\n" |
|
|
2444 |
] |
|
|
2445 |
}, |
|
|
2446 |
{ |
|
|
2447 |
"name": "stderr", |
|
|
2448 |
"output_type": "stream", |
|
|
2449 |
"text": [ |
|
|
2450 |
"COAD\n", |
|
|
2451 |
"TCGA-G4-6302-01A-11D-1717-01 has no genes with altered CN\n" |
|
|
2452 |
] |
|
|
2453 |
}, |
|
|
2454 |
{ |
|
|
2455 |
"name": "stdout", |
|
|
2456 |
"output_type": "stream", |
|
|
2457 |
"text": [ |
|
|
2458 |
"... 100 processed.\n" |
|
|
2459 |
] |
|
|
2460 |
}, |
|
|
2461 |
{ |
|
|
2462 |
"name": "stderr", |
|
|
2463 |
"output_type": "stream", |
|
|
2464 |
"text": [ |
|
|
2465 |
"TCGA-AA-A03F-01A-11D-A080-01 has no genes with altered CN\n" |
|
|
2466 |
] |
|
|
2467 |
}, |
|
|
2468 |
{ |
|
|
2469 |
"name": "stdout", |
|
|
2470 |
"output_type": "stream", |
|
|
2471 |
"text": [ |
|
|
2472 |
"... 200 processed.\n", |
|
|
2473 |
"... 300 processed.\n", |
|
|
2474 |
"... 400 processed.\n", |
|
|
2475 |
"COAD (36019, 453)\n" |
|
|
2476 |
] |
|
|
2477 |
}, |
|
|
2478 |
{ |
|
|
2479 |
"name": "stderr", |
|
|
2480 |
"output_type": "stream", |
|
|
2481 |
"text": [ |
|
|
2482 |
"ACC\n", |
|
|
2483 |
"TCGA-OR-A5KQ-01A-11D-A309-01 has no genes with altered CN\n", |
|
|
2484 |
"TCGA-OR-A5KV-01A-11D-A29H-01 has no genes with altered CN\n" |
|
|
2485 |
] |
|
|
2486 |
}, |
|
|
2487 |
{ |
|
|
2488 |
"name": "stdout", |
|
|
2489 |
"output_type": "stream", |
|
|
2490 |
"text": [ |
|
|
2491 |
"ACC (36019, 90)\n" |
|
|
2492 |
] |
|
|
2493 |
}, |
|
|
2494 |
{ |
|
|
2495 |
"name": "stderr", |
|
|
2496 |
"output_type": "stream", |
|
|
2497 |
"text": [ |
|
|
2498 |
"PAAD\n", |
|
|
2499 |
"TCGA-IB-AAUR-01A-21D-A38F-01 has no genes with altered CN\n", |
|
|
2500 |
"TCGA-HZ-8002-01A-11D-2200-01 has no genes with altered CN\n", |
|
|
2501 |
"TCGA-XD-AAUG-01A-61D-A40V-01 has no genes with altered CN\n", |
|
|
2502 |
"TCGA-Z5-AAPL-01A-12D-A40V-01 has no genes with altered CN\n", |
|
|
2503 |
"TCGA-IB-A5SQ-01A-11D-A32M-01 has no genes with altered CN\n" |
|
|
2504 |
] |
|
|
2505 |
}, |
|
|
2506 |
{ |
|
|
2507 |
"name": "stdout", |
|
|
2508 |
"output_type": "stream", |
|
|
2509 |
"text": [ |
|
|
2510 |
"... 100 processed.\n" |
|
|
2511 |
] |
|
|
2512 |
}, |
|
|
2513 |
{ |
|
|
2514 |
"name": "stderr", |
|
|
2515 |
"output_type": "stream", |
|
|
2516 |
"text": [ |
|
|
2517 |
"TCGA-IB-AAUS-01A-12D-A38F-01 has no genes with altered CN\n" |
|
|
2518 |
] |
|
|
2519 |
}, |
|
|
2520 |
{ |
|
|
2521 |
"name": "stdout", |
|
|
2522 |
"output_type": "stream", |
|
|
2523 |
"text": [ |
|
|
2524 |
"PAAD (36019, 185)\n" |
|
|
2525 |
] |
|
|
2526 |
}, |
|
|
2527 |
{ |
|
|
2528 |
"name": "stderr", |
|
|
2529 |
"output_type": "stream", |
|
|
2530 |
"text": [ |
|
|
2531 |
"THYM\n", |
|
|
2532 |
"TCGA-4V-A9QW-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2533 |
"TCGA-ZB-A96B-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2534 |
"TCGA-X7-A8DB-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2535 |
"TCGA-X7-A8M4-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2536 |
"TCGA-X7-A8D8-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2537 |
"TCGA-3S-AAYX-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2538 |
"TCGA-YT-A95E-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2539 |
"TCGA-X7-A8M8-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2540 |
"TCGA-ZT-A8OM-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2541 |
"TCGA-ZB-A96E-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2542 |
"TCGA-3Q-A9WF-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2543 |
"TCGA-X7-A8M1-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2544 |
"TCGA-ZB-A96A-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2545 |
"TCGA-ZB-A96R-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2546 |
"TCGA-ZB-A963-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2547 |
"TCGA-ZC-AAAA-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2548 |
"TCGA-XM-A8RB-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2549 |
"TCGA-ZB-A96G-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2550 |
"TCGA-X7-A8M7-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2551 |
"TCGA-XU-AAXZ-01A-11D-A427-01 has no genes with altered CN\n", |
|
|
2552 |
"TCGA-XH-A853-01A-11D-A422-01 has no genes with altered CN\n", |
|
|
2553 |
"TCGA-XM-AAZ3-01A-11D-A422-01 has no genes with altered CN\n" |
|
|
2554 |
] |
|
|
2555 |
}, |
|
|
2556 |
{ |
|
|
2557 |
"name": "stdout", |
|
|
2558 |
"output_type": "stream", |
|
|
2559 |
"text": [ |
|
|
2560 |
"... 100 processed.\n", |
|
|
2561 |
"THYM (36019, 125)\n" |
|
|
2562 |
] |
|
|
2563 |
}, |
|
|
2564 |
{ |
|
|
2565 |
"name": "stderr", |
|
|
2566 |
"output_type": "stream", |
|
|
2567 |
"text": [ |
|
|
2568 |
"LUSC\n", |
|
|
2569 |
"TCGA-56-8623-01A-11D-2391-01 has no genes with altered CN\n" |
|
|
2570 |
] |
|
|
2571 |
}, |
|
|
2572 |
{ |
|
|
2573 |
"name": "stdout", |
|
|
2574 |
"output_type": "stream", |
|
|
2575 |
"text": [ |
|
|
2576 |
"... 100 processed.\n", |
|
|
2577 |
"... 200 processed.\n", |
|
|
2578 |
"... 300 processed.\n", |
|
|
2579 |
"... 400 processed.\n" |
|
|
2580 |
] |
|
|
2581 |
}, |
|
|
2582 |
{ |
|
|
2583 |
"name": "stderr", |
|
|
2584 |
"output_type": "stream", |
|
|
2585 |
"text": [ |
|
|
2586 |
"TCGA-98-A53H-01A-12D-A25M-01 has no genes with altered CN\n" |
|
|
2587 |
] |
|
|
2588 |
}, |
|
|
2589 |
{ |
|
|
2590 |
"name": "stdout", |
|
|
2591 |
"output_type": "stream", |
|
|
2592 |
"text": [ |
|
|
2593 |
"LUSC (36019, 501)\n" |
|
|
2594 |
] |
|
|
2595 |
}, |
|
|
2596 |
{ |
|
|
2597 |
"name": "stderr", |
|
|
2598 |
"output_type": "stream", |
|
|
2599 |
"text": [ |
|
|
2600 |
"MESO\n", |
|
|
2601 |
"TCGA-TS-A8AS-01A-21D-A39Q-01 has no genes with altered CN\n", |
|
|
2602 |
"TCGA-TS-A7P8-01A-11D-A34B-01 has no genes with altered CN\n", |
|
|
2603 |
"TCGA-TS-A8AV-01A-12D-A39Q-01 has no genes with altered CN\n", |
|
|
2604 |
"TCGA-3H-AB3O-01A-11D-A39Q-01 has no genes with altered CN\n" |
|
|
2605 |
] |
|
|
2606 |
}, |
|
|
2607 |
{ |
|
|
2608 |
"name": "stdout", |
|
|
2609 |
"output_type": "stream", |
|
|
2610 |
"text": [ |
|
|
2611 |
"MESO (36019, 87)\n" |
|
|
2612 |
] |
|
|
2613 |
}, |
|
|
2614 |
{ |
|
|
2615 |
"name": "stderr", |
|
|
2616 |
"output_type": "stream", |
|
|
2617 |
"text": [ |
|
|
2618 |
"OV\n" |
|
|
2619 |
] |
|
|
2620 |
}, |
|
|
2621 |
{ |
|
|
2622 |
"name": "stdout", |
|
|
2623 |
"output_type": "stream", |
|
|
2624 |
"text": [ |
|
|
2625 |
"... 100 processed.\n", |
|
|
2626 |
"... 200 processed.\n", |
|
|
2627 |
"... 300 processed.\n", |
|
|
2628 |
"... 400 processed.\n", |
|
|
2629 |
"... 500 processed.\n", |
|
|
2630 |
"OV (36019, 597)\n" |
|
|
2631 |
] |
|
|
2632 |
}, |
|
|
2633 |
{ |
|
|
2634 |
"name": "stderr", |
|
|
2635 |
"output_type": "stream", |
|
|
2636 |
"text": [ |
|
|
2637 |
"SARC\n" |
|
|
2638 |
] |
|
|
2639 |
}, |
|
|
2640 |
{ |
|
|
2641 |
"name": "stdout", |
|
|
2642 |
"output_type": "stream", |
|
|
2643 |
"text": [ |
|
|
2644 |
"... 100 processed.\n" |
|
|
2645 |
] |
|
|
2646 |
}, |
|
|
2647 |
{ |
|
|
2648 |
"name": "stderr", |
|
|
2649 |
"output_type": "stream", |
|
|
2650 |
"text": [ |
|
|
2651 |
"TCGA-WK-A8Y0-10D-01D-A419-01 has no genes with altered CN\n" |
|
|
2652 |
] |
|
|
2653 |
}, |
|
|
2654 |
{ |
|
|
2655 |
"name": "stdout", |
|
|
2656 |
"output_type": "stream", |
|
|
2657 |
"text": [ |
|
|
2658 |
"... 200 processed.\n" |
|
|
2659 |
] |
|
|
2660 |
}, |
|
|
2661 |
{ |
|
|
2662 |
"name": "stderr", |
|
|
2663 |
"output_type": "stream", |
|
|
2664 |
"text": [ |
|
|
2665 |
"TCGA-WK-A8XS-10E-01D-A37E-01 has no genes with altered CN\n", |
|
|
2666 |
"TCGA-QQ-A5V2-01A-11D-A32H-01 has no genes with altered CN\n" |
|
|
2667 |
] |
|
|
2668 |
}, |
|
|
2669 |
{ |
|
|
2670 |
"name": "stdout", |
|
|
2671 |
"output_type": "stream", |
|
|
2672 |
"text": [ |
|
|
2673 |
"SARC (36019, 263)\n" |
|
|
2674 |
] |
|
|
2675 |
}, |
|
|
2676 |
{ |
|
|
2677 |
"name": "stderr", |
|
|
2678 |
"output_type": "stream", |
|
|
2679 |
"text": [ |
|
|
2680 |
"KIRP\n", |
|
|
2681 |
"TCGA-Y8-A8S1-01A-11D-A36W-01 has no genes with altered CN\n", |
|
|
2682 |
"TCGA-GL-A4EM-01A-11D-A253-01 has no genes with altered CN\n", |
|
|
2683 |
"TCGA-4A-A93Y-01A-11D-A36W-01 has no genes with altered CN\n", |
|
|
2684 |
"TCGA-AL-3467-01A-02D-1348-01 has no genes with altered CN\n" |
|
|
2685 |
] |
|
|
2686 |
}, |
|
|
2687 |
{ |
|
|
2688 |
"name": "stdout", |
|
|
2689 |
"output_type": "stream", |
|
|
2690 |
"text": [ |
|
|
2691 |
"... 100 processed.\n" |
|
|
2692 |
] |
|
|
2693 |
}, |
|
|
2694 |
{ |
|
|
2695 |
"name": "stderr", |
|
|
2696 |
"output_type": "stream", |
|
|
2697 |
"text": [ |
|
|
2698 |
"TCGA-A4-7828-01A-11D-2135-01 has no genes with altered CN\n", |
|
|
2699 |
"TCGA-DW-7838-01A-11D-2135-01 has no genes with altered CN\n" |
|
|
2700 |
] |
|
|
2701 |
}, |
|
|
2702 |
{ |
|
|
2703 |
"name": "stdout", |
|
|
2704 |
"output_type": "stream", |
|
|
2705 |
"text": [ |
|
|
2706 |
"... 200 processed.\n", |
|
|
2707 |
"KIRP (36019, 288)\n" |
|
|
2708 |
] |
|
|
2709 |
}, |
|
|
2710 |
{ |
|
|
2711 |
"name": "stderr", |
|
|
2712 |
"output_type": "stream", |
|
|
2713 |
"text": [ |
|
|
2714 |
"LGG\n", |
|
|
2715 |
"TCGA-HT-8106-01A-11D-2391-01 has no genes with altered CN\n", |
|
|
2716 |
"TCGA-S9-A6WI-01A-21D-A33S-01 has no genes with altered CN\n", |
|
|
2717 |
"TCGA-HT-7602-01A-21D-2085-01 has no genes with altered CN\n" |
|
|
2718 |
] |
|
|
2719 |
}, |
|
|
2720 |
{ |
|
|
2721 |
"name": "stdout", |
|
|
2722 |
"output_type": "stream", |
|
|
2723 |
"text": [ |
|
|
2724 |
"... 100 processed.\n" |
|
|
2725 |
] |
|
|
2726 |
}, |
|
|
2727 |
{ |
|
|
2728 |
"name": "stderr", |
|
|
2729 |
"output_type": "stream", |
|
|
2730 |
"text": [ |
|
|
2731 |
"TCGA-DU-7011-01A-11D-2023-01 has no genes with altered CN\n", |
|
|
2732 |
"TCGA-TM-A84B-12A-01D-A366-01 has no genes with altered CN\n" |
|
|
2733 |
] |
|
|
2734 |
}, |
|
|
2735 |
{ |
|
|
2736 |
"name": "stdout", |
|
|
2737 |
"output_type": "stream", |
|
|
2738 |
"text": [ |
|
|
2739 |
"... 200 processed.\n" |
|
|
2740 |
] |
|
|
2741 |
}, |
|
|
2742 |
{ |
|
|
2743 |
"name": "stderr", |
|
|
2744 |
"output_type": "stream", |
|
|
2745 |
"text": [ |
|
|
2746 |
"TCGA-FG-8181-01A-11D-2252-01 has no genes with altered CN\n" |
|
|
2747 |
] |
|
|
2748 |
}, |
|
|
2749 |
{ |
|
|
2750 |
"name": "stdout", |
|
|
2751 |
"output_type": "stream", |
|
|
2752 |
"text": [ |
|
|
2753 |
"... 300 processed.\n" |
|
|
2754 |
] |
|
|
2755 |
}, |
|
|
2756 |
{ |
|
|
2757 |
"name": "stderr", |
|
|
2758 |
"output_type": "stream", |
|
|
2759 |
"text": [ |
|
|
2760 |
"TCGA-FG-8189-01B-11D-A288-01 has no genes with altered CN\n" |
|
|
2761 |
] |
|
|
2762 |
}, |
|
|
2763 |
{ |
|
|
2764 |
"name": "stdout", |
|
|
2765 |
"output_type": "stream", |
|
|
2766 |
"text": [ |
|
|
2767 |
"... 400 processed.\n" |
|
|
2768 |
] |
|
|
2769 |
}, |
|
|
2770 |
{ |
|
|
2771 |
"name": "stderr", |
|
|
2772 |
"output_type": "stream", |
|
|
2773 |
"text": [ |
|
|
2774 |
"TCGA-DU-5872-02A-21D-A36N-01 has no genes with altered CN\n" |
|
|
2775 |
] |
|
|
2776 |
}, |
|
|
2777 |
{ |
|
|
2778 |
"name": "stdout", |
|
|
2779 |
"output_type": "stream", |
|
|
2780 |
"text": [ |
|
|
2781 |
"... 500 processed.\n" |
|
|
2782 |
] |
|
|
2783 |
}, |
|
|
2784 |
{ |
|
|
2785 |
"name": "stderr", |
|
|
2786 |
"output_type": "stream", |
|
|
2787 |
"text": [ |
|
|
2788 |
"TCGA-HT-7680-01A-11D-2252-01 has no genes with altered CN\n", |
|
|
2789 |
"TCGA-P5-A5EY-01A-11D-A27J-01 has no genes with altered CN\n", |
|
|
2790 |
"TCGA-CS-6669-01A-11D-1892-01 has no genes with altered CN\n" |
|
|
2791 |
] |
|
|
2792 |
}, |
|
|
2793 |
{ |
|
|
2794 |
"name": "stdout", |
|
|
2795 |
"output_type": "stream", |
|
|
2796 |
"text": [ |
|
|
2797 |
"LGG (36019, 530)\n" |
|
|
2798 |
] |
|
|
2799 |
}, |
|
|
2800 |
{ |
|
|
2801 |
"name": "stderr", |
|
|
2802 |
"output_type": "stream", |
|
|
2803 |
"text": [ |
|
|
2804 |
"LAML\n", |
|
|
2805 |
"TCGA-AB-2884-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2806 |
"TCGA-AB-2932-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2807 |
"TCGA-AB-2842-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2808 |
"TCGA-AB-2969-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2809 |
"TCGA-AB-2826-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2810 |
"TCGA-AB-2836-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2811 |
"TCGA-AB-2871-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2812 |
"TCGA-AB-2845-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2813 |
"TCGA-AB-2840-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2814 |
"TCGA-AB-2837-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2815 |
"TCGA-AB-2844-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2816 |
"TCGA-AB-2854-03A-01D-0756-21 has no genes with altered CN\n" |
|
|
2817 |
] |
|
|
2818 |
}, |
|
|
2819 |
{ |
|
|
2820 |
"name": "stdout", |
|
|
2821 |
"output_type": "stream", |
|
|
2822 |
"text": [ |
|
|
2823 |
"... 100 processed.\n" |
|
|
2824 |
] |
|
|
2825 |
}, |
|
|
2826 |
{ |
|
|
2827 |
"name": "stderr", |
|
|
2828 |
"output_type": "stream", |
|
|
2829 |
"text": [ |
|
|
2830 |
"TCGA-AB-3006-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2831 |
"TCGA-AB-2931-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2832 |
"TCGA-AB-2851-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2833 |
"TCGA-AB-2978-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2834 |
"TCGA-AB-2880-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2835 |
"TCGA-AB-2922-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2836 |
"TCGA-AB-2947-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2837 |
"TCGA-AB-2998-03A-01D-0756-21 has no genes with altered CN\n", |
|
|
2838 |
"TCGA-AB-2824-03A-01D-0756-21 has no genes with altered CN\n" |
|
|
2839 |
] |
|
|
2840 |
}, |
|
|
2841 |
{ |
|
|
2842 |
"name": "stdout", |
|
|
2843 |
"output_type": "stream", |
|
|
2844 |
"text": [ |
|
|
2845 |
"LAML (36019, 191)\n" |
|
|
2846 |
] |
|
|
2847 |
}, |
|
|
2848 |
{ |
|
|
2849 |
"name": "stderr", |
|
|
2850 |
"output_type": "stream", |
|
|
2851 |
"text": [ |
|
|
2852 |
"LIHC\n", |
|
|
2853 |
"TCGA-2V-A95S-10D-01D-A36Z-01 has no genes with altered CN\n", |
|
|
2854 |
"TCGA-UB-AA0V-01A-11D-A381-01 has no genes with altered CN\n" |
|
|
2855 |
] |
|
|
2856 |
}, |
|
|
2857 |
{ |
|
|
2858 |
"name": "stdout", |
|
|
2859 |
"output_type": "stream", |
|
|
2860 |
"text": [ |
|
|
2861 |
"... 100 processed.\n" |
|
|
2862 |
] |
|
|
2863 |
}, |
|
|
2864 |
{ |
|
|
2865 |
"name": "stderr", |
|
|
2866 |
"output_type": "stream", |
|
|
2867 |
"text": [ |
|
|
2868 |
"TCGA-G3-A25V-01A-11D-A16U-01 has no genes with altered CN\n", |
|
|
2869 |
"TCGA-DD-A3A6-01A-11D-A22E-01 has no genes with altered CN\n", |
|
|
2870 |
"TCGA-DD-A4NL-01A-11D-A28W-01 has no genes with altered CN\n" |
|
|
2871 |
] |
|
|
2872 |
}, |
|
|
2873 |
{ |
|
|
2874 |
"name": "stdout", |
|
|
2875 |
"output_type": "stream", |
|
|
2876 |
"text": [ |
|
|
2877 |
"... 200 processed.\n" |
|
|
2878 |
] |
|
|
2879 |
}, |
|
|
2880 |
{ |
|
|
2881 |
"name": "stderr", |
|
|
2882 |
"output_type": "stream", |
|
|
2883 |
"text": [ |
|
|
2884 |
"TCGA-ED-A5KG-01A-11D-A27H-01 has no genes with altered CN\n", |
|
|
2885 |
"TCGA-CC-A9FV-01A-11D-A36W-01 has no genes with altered CN\n" |
|
|
2886 |
] |
|
|
2887 |
}, |
|
|
2888 |
{ |
|
|
2889 |
"name": "stdout", |
|
|
2890 |
"output_type": "stream", |
|
|
2891 |
"text": [ |
|
|
2892 |
"... 300 processed.\n" |
|
|
2893 |
] |
|
|
2894 |
}, |
|
|
2895 |
{ |
|
|
2896 |
"name": "stderr", |
|
|
2897 |
"output_type": "stream", |
|
|
2898 |
"text": [ |
|
|
2899 |
"TCGA-MR-A520-01A-11D-A25U-01 has no genes with altered CN\n" |
|
|
2900 |
] |
|
|
2901 |
}, |
|
|
2902 |
{ |
|
|
2903 |
"name": "stdout", |
|
|
2904 |
"output_type": "stream", |
|
|
2905 |
"text": [ |
|
|
2906 |
"LIHC (36019, 373)\n" |
|
|
2907 |
] |
|
|
2908 |
}, |
|
|
2909 |
{ |
|
|
2910 |
"name": "stderr", |
|
|
2911 |
"output_type": "stream", |
|
|
2912 |
"text": [ |
|
|
2913 |
"PRAD\n", |
|
|
2914 |
"TCGA-J9-A52C-01A-11D-A26L-01 has no genes with altered CN\n", |
|
|
2915 |
"TCGA-V1-A8MJ-01A-11D-A363-01 has no genes with altered CN\n", |
|
|
2916 |
"TCGA-XJ-A9DQ-01A-11D-A376-01 has no genes with altered CN\n" |
|
|
2917 |
] |
|
|
2918 |
}, |
|
|
2919 |
{ |
|
|
2920 |
"name": "stdout", |
|
|
2921 |
"output_type": "stream", |
|
|
2922 |
"text": [ |
|
|
2923 |
"... 100 processed.\n" |
|
|
2924 |
] |
|
|
2925 |
}, |
|
|
2926 |
{ |
|
|
2927 |
"name": "stderr", |
|
|
2928 |
"output_type": "stream", |
|
|
2929 |
"text": [ |
|
|
2930 |
"TCGA-J4-A6G1-01A-11D-A30W-01 has no genes with altered CN\n" |
|
|
2931 |
] |
|
|
2932 |
}, |
|
|
2933 |
{ |
|
|
2934 |
"name": "stdout", |
|
|
2935 |
"output_type": "stream", |
|
|
2936 |
"text": [ |
|
|
2937 |
"... 200 processed.\n" |
|
|
2938 |
] |
|
|
2939 |
}, |
|
|
2940 |
{ |
|
|
2941 |
"name": "stderr", |
|
|
2942 |
"output_type": "stream", |
|
|
2943 |
"text": [ |
|
|
2944 |
"TCGA-J4-A67R-01A-21D-A30D-01 has no genes with altered CN\n", |
|
|
2945 |
"TCGA-EJ-A7NJ-01A-22D-A34T-01 has no genes with altered CN\n", |
|
|
2946 |
"TCGA-EJ-7791-01A-11D-2112-01 has no genes with altered CN\n" |
|
|
2947 |
] |
|
|
2948 |
}, |
|
|
2949 |
{ |
|
|
2950 |
"name": "stdout", |
|
|
2951 |
"output_type": "stream", |
|
|
2952 |
"text": [ |
|
|
2953 |
"... 300 processed.\n" |
|
|
2954 |
] |
|
|
2955 |
}, |
|
|
2956 |
{ |
|
|
2957 |
"name": "stderr", |
|
|
2958 |
"output_type": "stream", |
|
|
2959 |
"text": [ |
|
|
2960 |
"TCGA-EJ-A8FU-01A-11D-A363-01 has no genes with altered CN\n", |
|
|
2961 |
"TCGA-EJ-A6RC-01A-11D-A32A-01 has no genes with altered CN\n", |
|
|
2962 |
"TCGA-HC-7740-01A-11D-2112-01 has no genes with altered CN\n", |
|
|
2963 |
"TCGA-EJ-A65B-01A-12D-A30D-01 has no genes with altered CN\n", |
|
|
2964 |
"TCGA-HC-8260-01A-11D-2259-01 has no genes with altered CN\n", |
|
|
2965 |
"TCGA-FC-A8O0-01A-41D-A376-01 has no genes with altered CN\n" |
|
|
2966 |
] |
|
|
2967 |
}, |
|
|
2968 |
{ |
|
|
2969 |
"name": "stdout", |
|
|
2970 |
"output_type": "stream", |
|
|
2971 |
"text": [ |
|
|
2972 |
"... 400 processed.\n" |
|
|
2973 |
] |
|
|
2974 |
}, |
|
|
2975 |
{ |
|
|
2976 |
"name": "stderr", |
|
|
2977 |
"output_type": "stream", |
|
|
2978 |
"text": [ |
|
|
2979 |
"TCGA-VN-A88I-01A-11D-A34T-01 has no genes with altered CN\n", |
|
|
2980 |
"TCGA-EJ-A7NK-01A-12D-A34T-01 has no genes with altered CN\n", |
|
|
2981 |
"TCGA-CH-5743-01A-21D-1574-01 has no genes with altered CN\n", |
|
|
2982 |
"TCGA-G9-6367-01A-11D-1785-01 has no genes with altered CN\n", |
|
|
2983 |
"TCGA-KC-A4BO-01A-61D-A256-01 has no genes with altered CN\n" |
|
|
2984 |
] |
|
|
2985 |
}, |
|
|
2986 |
{ |
|
|
2987 |
"name": "stdout", |
|
|
2988 |
"output_type": "stream", |
|
|
2989 |
"text": [ |
|
|
2990 |
"PRAD (36019, 493)\n" |
|
|
2991 |
] |
|
|
2992 |
}, |
|
|
2993 |
{ |
|
|
2994 |
"name": "stderr", |
|
|
2995 |
"output_type": "stream", |
|
|
2996 |
"text": [ |
|
|
2997 |
"LUAD\n" |
|
|
2998 |
] |
|
|
2999 |
}, |
|
|
3000 |
{ |
|
|
3001 |
"name": "stdout", |
|
|
3002 |
"output_type": "stream", |
|
|
3003 |
"text": [ |
|
|
3004 |
"... 100 processed.\n", |
|
|
3005 |
"... 200 processed.\n" |
|
|
3006 |
] |
|
|
3007 |
}, |
|
|
3008 |
{ |
|
|
3009 |
"name": "stderr", |
|
|
3010 |
"output_type": "stream", |
|
|
3011 |
"text": [ |
|
|
3012 |
"TCGA-L4-A4E6-01A-11D-A24C-01 has no genes with altered CN\n" |
|
|
3013 |
] |
|
|
3014 |
}, |
|
|
3015 |
{ |
|
|
3016 |
"name": "stdout", |
|
|
3017 |
"output_type": "stream", |
|
|
3018 |
"text": [ |
|
|
3019 |
"... 300 processed.\n" |
|
|
3020 |
] |
|
|
3021 |
}, |
|
|
3022 |
{ |
|
|
3023 |
"name": "stderr", |
|
|
3024 |
"output_type": "stream", |
|
|
3025 |
"text": [ |
|
|
3026 |
"TCGA-44-3398-01A-01D-1877-01 has no genes with altered CN\n" |
|
|
3027 |
] |
|
|
3028 |
}, |
|
|
3029 |
{ |
|
|
3030 |
"name": "stdout", |
|
|
3031 |
"output_type": "stream", |
|
|
3032 |
"text": [ |
|
|
3033 |
"... 400 processed.\n" |
|
|
3034 |
] |
|
|
3035 |
}, |
|
|
3036 |
{ |
|
|
3037 |
"name": "stderr", |
|
|
3038 |
"output_type": "stream", |
|
|
3039 |
"text": [ |
|
|
3040 |
"TCGA-55-8619-01A-11D-2389-01 has no genes with altered CN\n", |
|
|
3041 |
"TCGA-86-A4P8-01A-11D-A24O-01 has no genes with altered CN\n" |
|
|
3042 |
] |
|
|
3043 |
}, |
|
|
3044 |
{ |
|
|
3045 |
"name": "stdout", |
|
|
3046 |
"output_type": "stream", |
|
|
3047 |
"text": [ |
|
|
3048 |
"... 500 processed.\n", |
|
|
3049 |
"LUAD (36019, 518)\n" |
|
|
3050 |
] |
|
|
3051 |
}, |
|
|
3052 |
{ |
|
|
3053 |
"name": "stderr", |
|
|
3054 |
"output_type": "stream", |
|
|
3055 |
"text": [ |
|
|
3056 |
"BRCA\n" |
|
|
3057 |
] |
|
|
3058 |
}, |
|
|
3059 |
{ |
|
|
3060 |
"name": "stdout", |
|
|
3061 |
"output_type": "stream", |
|
|
3062 |
"text": [ |
|
|
3063 |
"... 100 processed.\n" |
|
|
3064 |
] |
|
|
3065 |
}, |
|
|
3066 |
{ |
|
|
3067 |
"name": "stderr", |
|
|
3068 |
"output_type": "stream", |
|
|
3069 |
"text": [ |
|
|
3070 |
"TCGA-AO-A0JC-01A-11D-A059-01 has no genes with altered CN\n" |
|
|
3071 |
] |
|
|
3072 |
}, |
|
|
3073 |
{ |
|
|
3074 |
"name": "stdout", |
|
|
3075 |
"output_type": "stream", |
|
|
3076 |
"text": [ |
|
|
3077 |
"... 200 processed.\n" |
|
|
3078 |
] |
|
|
3079 |
}, |
|
|
3080 |
{ |
|
|
3081 |
"name": "stderr", |
|
|
3082 |
"output_type": "stream", |
|
|
3083 |
"text": [ |
|
|
3084 |
"TCGA-BH-A0H5-01A-21D-A111-01 has no genes with altered CN\n", |
|
|
3085 |
"TCGA-A2-A0CR-01A-11D-A227-01 has no genes with altered CN\n" |
|
|
3086 |
] |
|
|
3087 |
}, |
|
|
3088 |
{ |
|
|
3089 |
"name": "stdout", |
|
|
3090 |
"output_type": "stream", |
|
|
3091 |
"text": [ |
|
|
3092 |
"... 300 processed.\n" |
|
|
3093 |
] |
|
|
3094 |
}, |
|
|
3095 |
{ |
|
|
3096 |
"name": "stderr", |
|
|
3097 |
"output_type": "stream", |
|
|
3098 |
"text": [ |
|
|
3099 |
"TCGA-BH-A1FE-06A-11D-A20R-01 has no genes with altered CN\n", |
|
|
3100 |
"TCGA-AN-A0FN-01A-11D-A036-01 has no genes with altered CN\n" |
|
|
3101 |
] |
|
|
3102 |
}, |
|
|
3103 |
{ |
|
|
3104 |
"name": "stdout", |
|
|
3105 |
"output_type": "stream", |
|
|
3106 |
"text": [ |
|
|
3107 |
"... 400 processed.\n", |
|
|
3108 |
"... 500 processed.\n" |
|
|
3109 |
] |
|
|
3110 |
}, |
|
|
3111 |
{ |
|
|
3112 |
"name": "stderr", |
|
|
3113 |
"output_type": "stream", |
|
|
3114 |
"text": [ |
|
|
3115 |
"TCGA-PL-A8LY-01A-11D-A41E-01 has no genes with altered CN\n" |
|
|
3116 |
] |
|
|
3117 |
}, |
|
|
3118 |
{ |
|
|
3119 |
"name": "stdout", |
|
|
3120 |
"output_type": "stream", |
|
|
3121 |
"text": [ |
|
|
3122 |
"... 600 processed.\n", |
|
|
3123 |
"... 700 processed.\n" |
|
|
3124 |
] |
|
|
3125 |
}, |
|
|
3126 |
{ |
|
|
3127 |
"name": "stderr", |
|
|
3128 |
"output_type": "stream", |
|
|
3129 |
"text": [ |
|
|
3130 |
"TCGA-GM-A3XG-01A-31D-A242-01 has no genes with altered CN\n", |
|
|
3131 |
"TCGA-LD-A74U-01A-13D-A33D-01 has no genes with altered CN\n" |
|
|
3132 |
] |
|
|
3133 |
}, |
|
|
3134 |
{ |
|
|
3135 |
"name": "stdout", |
|
|
3136 |
"output_type": "stream", |
|
|
3137 |
"text": [ |
|
|
3138 |
"... 800 processed.\n" |
|
|
3139 |
] |
|
|
3140 |
}, |
|
|
3141 |
{ |
|
|
3142 |
"name": "stderr", |
|
|
3143 |
"output_type": "stream", |
|
|
3144 |
"text": [ |
|
|
3145 |
"TCGA-GM-A2DO-10D-01D-A18N-01 has no genes with altered CN\n", |
|
|
3146 |
"TCGA-A2-A0EP-01A-52D-A22W-01 has no genes with altered CN\n" |
|
|
3147 |
] |
|
|
3148 |
}, |
|
|
3149 |
{ |
|
|
3150 |
"name": "stdout", |
|
|
3151 |
"output_type": "stream", |
|
|
3152 |
"text": [ |
|
|
3153 |
"... 900 processed.\n", |
|
|
3154 |
"... 1000 processed.\n" |
|
|
3155 |
] |
|
|
3156 |
}, |
|
|
3157 |
{ |
|
|
3158 |
"name": "stderr", |
|
|
3159 |
"output_type": "stream", |
|
|
3160 |
"text": [ |
|
|
3161 |
"TCGA-AO-A1KO-01A-31D-A13J-01 has no genes with altered CN\n" |
|
|
3162 |
] |
|
|
3163 |
}, |
|
|
3164 |
{ |
|
|
3165 |
"name": "stdout", |
|
|
3166 |
"output_type": "stream", |
|
|
3167 |
"text": [ |
|
|
3168 |
"BRCA (36019, 1088)\n" |
|
|
3169 |
] |
|
|
3170 |
}, |
|
|
3171 |
{ |
|
|
3172 |
"name": "stderr", |
|
|
3173 |
"output_type": "stream", |
|
|
3174 |
"text": [ |
|
|
3175 |
"KIRC\n", |
|
|
3176 |
"TCGA-B4-5378-01A-01D-1499-01 has no genes with altered CN\n", |
|
|
3177 |
"TCGA-B0-5400-01A-01D-1499-01 has no genes with altered CN\n", |
|
|
3178 |
"TCGA-CJ-4890-01A-01D-1302-01 has no genes with altered CN\n" |
|
|
3179 |
] |
|
|
3180 |
}, |
|
|
3181 |
{ |
|
|
3182 |
"name": "stdout", |
|
|
3183 |
"output_type": "stream", |
|
|
3184 |
"text": [ |
|
|
3185 |
"... 100 processed.\n" |
|
|
3186 |
] |
|
|
3187 |
}, |
|
|
3188 |
{ |
|
|
3189 |
"name": "stderr", |
|
|
3190 |
"output_type": "stream", |
|
|
3191 |
"text": [ |
|
|
3192 |
"TCGA-A3-A8OX-01A-11D-A36W-01 has no genes with altered CN\n", |
|
|
3193 |
"TCGA-B0-4817-01A-01D-1274-01 has no genes with altered CN\n", |
|
|
3194 |
"TCGA-B0-5080-01A-01D-1499-01 has no genes with altered CN\n" |
|
|
3195 |
] |
|
|
3196 |
}, |
|
|
3197 |
{ |
|
|
3198 |
"name": "stdout", |
|
|
3199 |
"output_type": "stream", |
|
|
3200 |
"text": [ |
|
|
3201 |
"... 200 processed.\n" |
|
|
3202 |
] |
|
|
3203 |
}, |
|
|
3204 |
{ |
|
|
3205 |
"name": "stderr", |
|
|
3206 |
"output_type": "stream", |
|
|
3207 |
"text": [ |
|
|
3208 |
"TCGA-DV-A4VZ-01A-11D-A25U-01 has no genes with altered CN\n" |
|
|
3209 |
] |
|
|
3210 |
}, |
|
|
3211 |
{ |
|
|
3212 |
"name": "stdout", |
|
|
3213 |
"output_type": "stream", |
|
|
3214 |
"text": [ |
|
|
3215 |
"... 300 processed.\n" |
|
|
3216 |
] |
|
|
3217 |
}, |
|
|
3218 |
{ |
|
|
3219 |
"name": "stderr", |
|
|
3220 |
"output_type": "stream", |
|
|
3221 |
"text": [ |
|
|
3222 |
"TCGA-CJ-4891-01A-01D-1302-01 has no genes with altered CN\n", |
|
|
3223 |
"TCGA-CJ-4889-01A-01D-1302-01 has no genes with altered CN\n", |
|
|
3224 |
"TCGA-BP-4769-01A-01D-1283-01 has no genes with altered CN\n" |
|
|
3225 |
] |
|
|
3226 |
}, |
|
|
3227 |
{ |
|
|
3228 |
"name": "stdout", |
|
|
3229 |
"output_type": "stream", |
|
|
3230 |
"text": [ |
|
|
3231 |
"... 400 processed.\n" |
|
|
3232 |
] |
|
|
3233 |
}, |
|
|
3234 |
{ |
|
|
3235 |
"name": "stderr", |
|
|
3236 |
"output_type": "stream", |
|
|
3237 |
"text": [ |
|
|
3238 |
"TCGA-BP-4760-01A-02D-1417-01 has no genes with altered CN\n" |
|
|
3239 |
] |
|
|
3240 |
}, |
|
|
3241 |
{ |
|
|
3242 |
"name": "stdout", |
|
|
3243 |
"output_type": "stream", |
|
|
3244 |
"text": [ |
|
|
3245 |
"... 500 processed.\n", |
|
|
3246 |
"KIRC (36019, 529)\n" |
|
|
3247 |
] |
|
|
3248 |
}, |
|
|
3249 |
{ |
|
|
3250 |
"name": "stderr", |
|
|
3251 |
"output_type": "stream", |
|
|
3252 |
"text": [ |
|
|
3253 |
"KICH\n" |
|
|
3254 |
] |
|
|
3255 |
}, |
|
|
3256 |
{ |
|
|
3257 |
"name": "stdout", |
|
|
3258 |
"output_type": "stream", |
|
|
3259 |
"text": [ |
|
|
3260 |
"KICH (36019, 66)\n" |
|
|
3261 |
] |
|
|
3262 |
} |
|
|
3263 |
], |
|
|
3264 |
"source": [ |
|
|
3265 |
"for cohort in dfs.keys():\n", |
|
|
3266 |
" print(cohort, file=sys.stderr)\n", |
|
|
3267 |
" df = dfs[cohort]\n", |
|
|
3268 |
" cna_table = []\n", |
|
|
3269 |
" n_samples = 0\n", |
|
|
3270 |
" for sample in list(set(df.Sample.values)):\n", |
|
|
3271 |
" n_samples +=1\n", |
|
|
3272 |
" cnv2gene = cnv2genelevel(cnv2bed(df[df.Sample == sample]),gene_intervals_bed,sample,\n", |
|
|
3273 |
" verbose = False,sorted_index = sorted_index)\n", |
|
|
3274 |
" cna_table.append(cnv2gene)\n", |
|
|
3275 |
" if n_samples % 100 == 0:\n", |
|
|
3276 |
" print(\"...\",n_samples, \"processed.\")\n", |
|
|
3277 |
" cna_table = pd.concat(cna_table,axis =1)\n", |
|
|
3278 |
" \n", |
|
|
3279 |
"\n", |
|
|
3280 |
" for sample in tumors_without_CNA[cohort]:\n", |
|
|
3281 |
" cna_table[sample] = 0\n", |
|
|
3282 |
" \n", |
|
|
3283 |
" cna_table.fillna(0, inplace = True)\n", |
|
|
3284 |
" cna_table.to_csv(preprocessed_dir+\"/TCGA-\"+cohort+\".Segment_Mean.CNA.tsv\",\n", |
|
|
3285 |
" sep = \"\\t\",header=True,index=True)\n", |
|
|
3286 |
" print(cohort,cna_table.shape)\n" |
|
|
3287 |
] |
|
|
3288 |
}, |
|
|
3289 |
{ |
|
|
3290 |
"cell_type": "code", |
|
|
3291 |
"execution_count": 14, |
|
|
3292 |
"metadata": {}, |
|
|
3293 |
"outputs": [ |
|
|
3294 |
{ |
|
|
3295 |
"data": { |
|
|
3296 |
"text/plain": [ |
|
|
3297 |
"'t = time.time()\\ncnv2gene = cnv2genelevel(cnv2bed(df[df.Sample == sample]),gene_intervals_bed,sample,\\n verbose = False,sorted_index = sorted_index)\\nprint( time.time() - t)\\ncnv2gene'" |
|
|
3298 |
] |
|
|
3299 |
}, |
|
|
3300 |
"execution_count": 14, |
|
|
3301 |
"metadata": {}, |
|
|
3302 |
"output_type": "execute_result" |
|
|
3303 |
} |
|
|
3304 |
], |
|
|
3305 |
"source": [ |
|
|
3306 |
"\"\"\"t = time.time()\n", |
|
|
3307 |
"cnv2gene = cnv2genelevel(cnv2bed(df[df.Sample == sample]),gene_intervals_bed,sample,\n", |
|
|
3308 |
" verbose = False,sorted_index = sorted_index)\n", |
|
|
3309 |
"print( time.time() - t)\n", |
|
|
3310 |
"cnv2gene\"\"\"" |
|
|
3311 |
] |
|
|
3312 |
}, |
|
|
3313 |
{ |
|
|
3314 |
"cell_type": "markdown", |
|
|
3315 |
"metadata": {}, |
|
|
3316 |
"source": [ |
|
|
3317 |
"# CCLE \n", |
|
|
3318 |
"\n", |
|
|
3319 |
"the same pipeline as for TCGA except filtering out germline CNA (because no )\n", |
|
|
3320 |
"\n", |
|
|
3321 |
"wget https://data.broadinstitute.org/ccle_legacy_data/dna_copy_number/CCLE_copynumber_2013-12-03.seg.txt\n", |
|
|
3322 |
"\n", |
|
|
3323 |
"? should we use a stronger segment_mean threshold because this data are for cell lines and purity must be 100%" |
|
|
3324 |
] |
|
|
3325 |
}, |
|
|
3326 |
{ |
|
|
3327 |
"cell_type": "code", |
|
|
3328 |
"execution_count": 15, |
|
|
3329 |
"metadata": { |
|
|
3330 |
"scrolled": true |
|
|
3331 |
}, |
|
|
3332 |
"outputs": [ |
|
|
3333 |
{ |
|
|
3334 |
"name": "stdout", |
|
|
3335 |
"output_type": "stream", |
|
|
3336 |
"text": [ |
|
|
3337 |
"47 duplicated IDs in 94 rows found.\n", |
|
|
3338 |
"duplicate rows removed due to low correlation of duplicated profiles 0\n", |
|
|
3339 |
"Merged 94 duplicated rows into 47 rows\n", |
|
|
3340 |
"CCLE: genes: 35972 samples 1043\n" |
|
|
3341 |
] |
|
|
3342 |
} |
|
|
3343 |
], |
|
|
3344 |
"source": [ |
|
|
3345 |
"df = pd.read_csv(\"../../CCLE/CCLE_copynumber_2013-12-03.seg.txt\",sep = \"\\t\")\n", |
|
|
3346 |
"df.rename({\"CCLE_name\":\"Sample\"},inplace=True, axis=\"columns\")\n", |
|
|
3347 |
"df[\"End\"] = df[\"End\"].apply(int)\n", |
|
|
3348 |
"ccle = []\n", |
|
|
3349 |
"for sample_name in list(set(df[\"Sample\"].values)):\n", |
|
|
3350 |
" cl = df.loc[df[\"Sample\"]==sample_name, :]\n", |
|
|
3351 |
" # keep high-conf segments \n", |
|
|
3352 |
" cl_filtered = filter_lowconf_segments(cl,num_marker_thr,pos_seg_mean_thr, neg_seg_mean_thr )\n", |
|
|
3353 |
" #print(sample_name, cl.shape[0], \"after filtration\",cl_filtered.shape[0])\n", |
|
|
3354 |
" # map to genes \n", |
|
|
3355 |
" cnv2gene = cnv2genelevel(cnv2bed(cl_filtered),gene_intervals_bed,sample_name,\n", |
|
|
3356 |
" verbose = False,sorted_index = sorted_index)\n", |
|
|
3357 |
" ccle.append(cnv2gene)\n", |
|
|
3358 |
" \n", |
|
|
3359 |
"ccle = pd.concat(ccle,axis =1)\n", |
|
|
3360 |
"ccle.fillna(0, inplace = True)\n", |
|
|
3361 |
"ccle = handle_dups(ccle)\n", |
|
|
3362 |
"ccle.to_csv(preprocessed_dir+\"/\"+\"CCLE\"+\".Segment_Mean.CNA.tsv\",\n", |
|
|
3363 |
" sep = \"\\t\",header=True,index=True)\n", |
|
|
3364 |
"print(\"CCLE:\",\"genes:\",ccle.shape[0],\"samples\",ccle.shape[1])" |
|
|
3365 |
] |
|
|
3366 |
}, |
|
|
3367 |
{ |
|
|
3368 |
"cell_type": "markdown", |
|
|
3369 |
"metadata": {}, |
|
|
3370 |
"source": [ |
|
|
3371 |
"# GDSC\n", |
|
|
3372 |
"Assume that supplementary file with gene-level CN is downloaded :\n", |
|
|
3373 |
"\n", |
|
|
3374 |
"wget \n", |
|
|
3375 |
"\n", |
|
|
3376 |
"GDSC provides gene-level integer estimated CN, max. and min. CN over all segments covering a gene. In order to make it comparable with TCGA and CCLE, we divide estimated CN by CN of copy-neutral state and log2-transform it. \n", |
|
|
3377 |
"\n", |
|
|
3378 |
"1) Copy-neutral state was defined from average ploiy, as median of integer CN values in non-disrupted genes.\n", |
|
|
3379 |
"\n", |
|
|
3380 |
"2) Compute log2(CN/neutral-CN) for min and max CN; keep the value with most extreme estimate\n", |
|
|
3381 |
"\n", |
|
|
3382 |
"3) Replace estimates below thresholds with zeroes. \n", |
|
|
3383 |
"\n", |
|
|
3384 |
"\n", |
|
|
3385 |
"DGSC uses 4 comma-separated values for gene-level CN (max_cn,min_cn,zygosity,disruption): e.g. (from \"legend\" tab)\n", |
|
|
3386 |
"\n", |
|
|
3387 |
"2,2,H,-\tGene resides on a single genomic segment in a diploid region of the genome.\n", |
|
|
3388 |
"2,0,L,D\tGene spans multiple segments, higest copy number is 2 but part of the coding sequence is homozygously deleted, the gene is disrupted.\n", |
|
|
3389 |
"13,13,H,-\tGene resides on a single genomic segment of copy number 13 in a heterozygous part of the genome (amplification).\n", |
|
|
3390 |
"14,12,L,D\tGene spans multiple genomic segments all of which are amplified to 12 or more copies, some or all segments have LOH, the gene is disrupted.\n", |
|
|
3391 |
"0,0,0,-\tComplete gene sequence falls within a homozygous deletion.\n", |
|
|
3392 |
"-1,-1,-,- gene level CN not assigned\n", |
|
|
3393 |
"\n", |
|
|
3394 |
"* min and max CN are integers \n", |
|
|
3395 |
"* zygosity - can be L (LOH in any overlapping segment) or H (heterozygous) or 0 (homozygous deleteion of the whole gene) or - (undefined)\n", |
|
|
3396 |
"* disruption - D (if disrupted) or \"-\" (not disrupted) \n", |
|
|
3397 |
"\n", |
|
|
3398 |
"Average ploidies of cell lines were downloaded from COSMIC:\n", |
|
|
3399 |
"\n", |
|
|
3400 |
"wget https://cog.sanger.ac.uk/cosmic/GRCh37/cell_lines/v86/PICNIC_average_ploidies.tsv?AWSAccessKeyId=KRV7P7QR9DL41J9EWGA2&Expires=1540792525&Signature=mcSB6oFv%2BXCF4%2Fezm4a3Ds1JXo4%3D\n", |
|
|
3401 |
"\n", |
|
|
3402 |
"wget ftp:// ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/release-7.0/Gene_level_CN.xlsx\n" |
|
|
3403 |
] |
|
|
3404 |
}, |
|
|
3405 |
{ |
|
|
3406 |
"cell_type": "code", |
|
|
3407 |
"execution_count": 16, |
|
|
3408 |
"metadata": {}, |
|
|
3409 |
"outputs": [ |
|
|
3410 |
{ |
|
|
3411 |
"data": { |
|
|
3412 |
"text/html": [ |
|
|
3413 |
"<div>\n", |
|
|
3414 |
"<style scoped>\n", |
|
|
3415 |
" .dataframe tbody tr th:only-of-type {\n", |
|
|
3416 |
" vertical-align: middle;\n", |
|
|
3417 |
" }\n", |
|
|
3418 |
"\n", |
|
|
3419 |
" .dataframe tbody tr th {\n", |
|
|
3420 |
" vertical-align: top;\n", |
|
|
3421 |
" }\n", |
|
|
3422 |
"\n", |
|
|
3423 |
" .dataframe thead th {\n", |
|
|
3424 |
" text-align: right;\n", |
|
|
3425 |
" }\n", |
|
|
3426 |
"</style>\n", |
|
|
3427 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
3428 |
" <thead>\n", |
|
|
3429 |
" <tr style=\"text-align: right;\">\n", |
|
|
3430 |
" <th></th>\n", |
|
|
3431 |
" <th>gene</th>\n", |
|
|
3432 |
" <th>chr</th>\n", |
|
|
3433 |
" <th>start</th>\n", |
|
|
3434 |
" <th>stop</th>\n", |
|
|
3435 |
" <th>201T</th>\n", |
|
|
3436 |
" <th>22RV1</th>\n", |
|
|
3437 |
" <th>23132-87</th>\n", |
|
|
3438 |
" <th>42-MG-BA</th>\n", |
|
|
3439 |
" <th>451Lu</th>\n", |
|
|
3440 |
" <th>5637</th>\n", |
|
|
3441 |
" <th>...</th>\n", |
|
|
3442 |
" <th>WSU-NHL</th>\n", |
|
|
3443 |
" <th>YAPC</th>\n", |
|
|
3444 |
" <th>YH-13</th>\n", |
|
|
3445 |
" <th>YKG-1</th>\n", |
|
|
3446 |
" <th>YMB-1-E</th>\n", |
|
|
3447 |
" <th>YT</th>\n", |
|
|
3448 |
" <th>ZR-75-30</th>\n", |
|
|
3449 |
" <th>huH-1</th>\n", |
|
|
3450 |
" <th>no-10</th>\n", |
|
|
3451 |
" <th>no-11</th>\n", |
|
|
3452 |
" </tr>\n", |
|
|
3453 |
" </thead>\n", |
|
|
3454 |
" <tbody>\n", |
|
|
3455 |
" <tr>\n", |
|
|
3456 |
" <th>0</th>\n", |
|
|
3457 |
" <td>NaN</td>\n", |
|
|
3458 |
" <td>NaN</td>\n", |
|
|
3459 |
" <td>NaN</td>\n", |
|
|
3460 |
" <td>NaN</td>\n", |
|
|
3461 |
" <td>1287381</td>\n", |
|
|
3462 |
" <td>924100</td>\n", |
|
|
3463 |
" <td>910924</td>\n", |
|
|
3464 |
" <td>687561</td>\n", |
|
|
3465 |
" <td>1287706</td>\n", |
|
|
3466 |
" <td>687452</td>\n", |
|
|
3467 |
" <td>...</td>\n", |
|
|
3468 |
" <td>909785</td>\n", |
|
|
3469 |
" <td>909904</td>\n", |
|
|
3470 |
" <td>909905</td>\n", |
|
|
3471 |
" <td>687592</td>\n", |
|
|
3472 |
" <td>1303911</td>\n", |
|
|
3473 |
" <td>946358</td>\n", |
|
|
3474 |
" <td>909907</td>\n", |
|
|
3475 |
" <td>1298146</td>\n", |
|
|
3476 |
" <td>908452</td>\n", |
|
|
3477 |
" <td>908450</td>\n", |
|
|
3478 |
" </tr>\n", |
|
|
3479 |
" <tr>\n", |
|
|
3480 |
" <th>1</th>\n", |
|
|
3481 |
" <td>DDX11L1</td>\n", |
|
|
3482 |
" <td>1</td>\n", |
|
|
3483 |
" <td>11869.0</td>\n", |
|
|
3484 |
" <td>14412.0</td>\n", |
|
|
3485 |
" <td>-1,-1,-,-</td>\n", |
|
|
3486 |
" <td>-1,-1,-,-</td>\n", |
|
|
3487 |
" <td>-1,-1,-,-</td>\n", |
|
|
3488 |
" <td>-1,-1,-,-</td>\n", |
|
|
3489 |
" <td>-1,-1,-,-</td>\n", |
|
|
3490 |
" <td>-1,-1,-,-</td>\n", |
|
|
3491 |
" <td>...</td>\n", |
|
|
3492 |
" <td>-1,-1,-,-</td>\n", |
|
|
3493 |
" <td>-1,-1,-,-</td>\n", |
|
|
3494 |
" <td>-1,-1,-,-</td>\n", |
|
|
3495 |
" <td>-1,-1,-,-</td>\n", |
|
|
3496 |
" <td>-1,-1,-,-</td>\n", |
|
|
3497 |
" <td>-1,-1,-,-</td>\n", |
|
|
3498 |
" <td>-1,-1,-,-</td>\n", |
|
|
3499 |
" <td>-1,-1,-,-</td>\n", |
|
|
3500 |
" <td>-1,-1,-,-</td>\n", |
|
|
3501 |
" <td>-1,-1,-,-</td>\n", |
|
|
3502 |
" </tr>\n", |
|
|
3503 |
" <tr>\n", |
|
|
3504 |
" <th>2</th>\n", |
|
|
3505 |
" <td>WASH7P</td>\n", |
|
|
3506 |
" <td>1</td>\n", |
|
|
3507 |
" <td>14363.0</td>\n", |
|
|
3508 |
" <td>29806.0</td>\n", |
|
|
3509 |
" <td>-1,-1,-,-</td>\n", |
|
|
3510 |
" <td>-1,-1,-,-</td>\n", |
|
|
3511 |
" <td>-1,-1,-,-</td>\n", |
|
|
3512 |
" <td>-1,-1,-,-</td>\n", |
|
|
3513 |
" <td>-1,-1,-,-</td>\n", |
|
|
3514 |
" <td>-1,-1,-,-</td>\n", |
|
|
3515 |
" <td>...</td>\n", |
|
|
3516 |
" <td>-1,-1,-,-</td>\n", |
|
|
3517 |
" <td>-1,-1,-,-</td>\n", |
|
|
3518 |
" <td>-1,-1,-,-</td>\n", |
|
|
3519 |
" <td>-1,-1,-,-</td>\n", |
|
|
3520 |
" <td>-1,-1,-,-</td>\n", |
|
|
3521 |
" <td>-1,-1,-,-</td>\n", |
|
|
3522 |
" <td>-1,-1,-,-</td>\n", |
|
|
3523 |
" <td>-1,-1,-,-</td>\n", |
|
|
3524 |
" <td>-1,-1,-,-</td>\n", |
|
|
3525 |
" <td>-1,-1,-,-</td>\n", |
|
|
3526 |
" </tr>\n", |
|
|
3527 |
" </tbody>\n", |
|
|
3528 |
"</table>\n", |
|
|
3529 |
"<p>3 rows × 1000 columns</p>\n", |
|
|
3530 |
"</div>" |
|
|
3531 |
], |
|
|
3532 |
"text/plain": [ |
|
|
3533 |
" gene chr start stop 201T 22RV1 23132-87 42-MG-BA \\\n", |
|
|
3534 |
"0 NaN NaN NaN NaN 1287381 924100 910924 687561 \n", |
|
|
3535 |
"1 DDX11L1 1 11869.0 14412.0 -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3536 |
"2 WASH7P 1 14363.0 29806.0 -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3537 |
"\n", |
|
|
3538 |
" 451Lu 5637 ... WSU-NHL YAPC YH-13 \\\n", |
|
|
3539 |
"0 1287706 687452 ... 909785 909904 909905 \n", |
|
|
3540 |
"1 -1,-1,-,- -1,-1,-,- ... -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3541 |
"2 -1,-1,-,- -1,-1,-,- ... -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3542 |
"\n", |
|
|
3543 |
" YKG-1 YMB-1-E YT ZR-75-30 huH-1 no-10 no-11 \n", |
|
|
3544 |
"0 687592 1303911 946358 909907 1298146 908452 908450 \n", |
|
|
3545 |
"1 -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3546 |
"2 -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- -1,-1,-,- \n", |
|
|
3547 |
"\n", |
|
|
3548 |
"[3 rows x 1000 columns]" |
|
|
3549 |
] |
|
|
3550 |
}, |
|
|
3551 |
"execution_count": 16, |
|
|
3552 |
"metadata": {}, |
|
|
3553 |
"output_type": "execute_result" |
|
|
3554 |
} |
|
|
3555 |
], |
|
|
3556 |
"source": [ |
|
|
3557 |
"GDSC_CNA = \"/home/olya/SFU/Hossein/GDSC/Gene_level_CN.xlsx\"\n", |
|
|
3558 |
"\n", |
|
|
3559 |
"gdsc = pd.read_excel(GDSC_CNA,\"Gene_level_CN\")\n", |
|
|
3560 |
"gdsc.head(3)" |
|
|
3561 |
] |
|
|
3562 |
}, |
|
|
3563 |
{ |
|
|
3564 |
"cell_type": "code", |
|
|
3565 |
"execution_count": 17, |
|
|
3566 |
"metadata": {}, |
|
|
3567 |
"outputs": [ |
|
|
3568 |
{ |
|
|
3569 |
"name": "stdout", |
|
|
3570 |
"output_type": "stream", |
|
|
3571 |
"text": [ |
|
|
3572 |
"25 gene IDs excluded due to string to datetime conversion in Excel.\n", |
|
|
3573 |
"Strings containing duplicated gene IDs: 0\n" |
|
|
3574 |
] |
|
|
3575 |
} |
|
|
3576 |
], |
|
|
3577 |
"source": [ |
|
|
3578 |
"gdsc.set_index(\"gene\",inplace = True)\n", |
|
|
3579 |
"gdsc.drop([\"chr\",\"start\",\"stop\"],inplace=True,axis=1)\n", |
|
|
3580 |
"gdsc.columns = gdsc.iloc[0,:]\n", |
|
|
3581 |
"gdsc = gdsc.iloc[1:,:]\n", |
|
|
3582 |
"gdsc.columns.name = None\n", |
|
|
3583 |
"# replace 2001-12-01 with DEC1 and get remove gene names converted to datetimes\n", |
|
|
3584 |
"gdsc.index.values[37778] = \"DEC1\"\n", |
|
|
3585 |
"df_size = gdsc.shape[0]\n", |
|
|
3586 |
"ndxs=pd.Series(gdsc.index).apply(lambda x : type(x) == unicode or type(x) == str)\n", |
|
|
3587 |
"gdsc = gdsc.loc[gdsc.index.values[ndxs[ndxs].index],:]\n", |
|
|
3588 |
"print(df_size - gdsc.shape[0],\"gene IDs excluded due to string to datetime conversion in Excel.\")\n", |
|
|
3589 |
"\n", |
|
|
3590 |
"gdsc.index.name = \"gene_id\"\n", |
|
|
3591 |
"ids = gdsc.index\n", |
|
|
3592 |
"ids = list(set(ids[ids.duplicated()]))\n", |
|
|
3593 |
"print(\"Strings containing duplicated gene IDs:\",gdsc.loc[ids,:].shape[0])" |
|
|
3594 |
] |
|
|
3595 |
}, |
|
|
3596 |
{ |
|
|
3597 |
"cell_type": "markdown", |
|
|
3598 |
"metadata": {}, |
|
|
3599 |
"source": [ |
|
|
3600 |
"### distribution of averaged ploidies in GDSC\n", |
|
|
3601 |
"\n", |
|
|
3602 |
"we compared average ploidies reported in PICNIC_average_ploidies.tsv provided by COSMIC with " |
|
|
3603 |
] |
|
|
3604 |
}, |
|
|
3605 |
{ |
|
|
3606 |
"cell_type": "code", |
|
|
3607 |
"execution_count": 18, |
|
|
3608 |
"metadata": {}, |
|
|
3609 |
"outputs": [ |
|
|
3610 |
{ |
|
|
3611 |
"name": "stdout", |
|
|
3612 |
"output_type": "stream", |
|
|
3613 |
"text": [ |
|
|
3614 |
"1020\n", |
|
|
3615 |
"1016\n" |
|
|
3616 |
] |
|
|
3617 |
} |
|
|
3618 |
], |
|
|
3619 |
"source": [ |
|
|
3620 |
"GDSC_Ploidies = \"/home/olya/SFU/Hossein/GDSC/PICNIC_average_ploidies.tsv\"\n", |
|
|
3621 |
"GDSC_Ploidies = pd.read_csv(GDSC_Ploidies,sep = \"\\t\")\n", |
|
|
3622 |
"GDSC_Ploidies.drop(\"#sample_name\",axis = 1, inplace= True)\n", |
|
|
3623 |
"GDSC_Ploidies.set_index(\"sample_id\",inplace=True)\n", |
|
|
3624 |
"print(GDSC_Ploidies.shape[0])\n", |
|
|
3625 |
"GDSC_Ploidies.dropna(inplace=True)\n", |
|
|
3626 |
"print(GDSC_Ploidies.shape[0])\n", |
|
|
3627 |
"\n", |
|
|
3628 |
"est_ploidies = gdsc.apply(define_avg_ploidy).T\n", |
|
|
3629 |
"df_ploidies = pd.DataFrame.from_dict({\"est. avg. ploidy from CN profile\":est_ploidies[\"avg_pl\"],\"PICNIC avg. pl.\":GDSC_Ploidies[\"average_ploidy\"],\n", |
|
|
3630 |
" \"est. median. ploidy\":est_ploidies[\"median_pl\"]})\n" |
|
|
3631 |
] |
|
|
3632 |
}, |
|
|
3633 |
{ |
|
|
3634 |
"cell_type": "code", |
|
|
3635 |
"execution_count": 19, |
|
|
3636 |
"metadata": {}, |
|
|
3637 |
"outputs": [ |
|
|
3638 |
{ |
|
|
3639 |
"data": { |
|
|
3640 |
"image/png": 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\n", |
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3641 |
"text/plain": [ |
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3642 |
"<Figure size 1440x360 with 3 Axes>" |
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3643 |
] |
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3644 |
}, |
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|
3645 |
"metadata": {}, |
|
|
3646 |
"output_type": "display_data" |
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3647 |
}, |
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3648 |
{ |
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3649 |
"data": { |
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3650 |
"image/png": 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\n", |
|
|
3651 |
"text/plain": [ |
|
|
3652 |
"<Figure size 432x288 with 1 Axes>" |
|
|
3653 |
] |
|
|
3654 |
}, |
|
|
3655 |
"metadata": {}, |
|
|
3656 |
"output_type": "display_data" |
|
|
3657 |
} |
|
|
3658 |
], |
|
|
3659 |
"source": [ |
|
|
3660 |
"plt.figure(figsize=(20,5))\n", |
|
|
3661 |
"plt.subplot(131)\n", |
|
|
3662 |
"tmp = plt.hist(est_ploidies[\"avg_pl\"],bins=30)\n", |
|
|
3663 |
"plt.title(\"est. avg. ploidy from CN profile\")\n", |
|
|
3664 |
"plt.subplot(132)\n", |
|
|
3665 |
"tmp = plt.hist(sorted(list(GDSC_Ploidies[\"average_ploidy\"].values)),bins=30)\n", |
|
|
3666 |
"plt.title(\"PICNIC avg. pl.\")\n", |
|
|
3667 |
"plt.subplot(133)\n", |
|
|
3668 |
"tmp = plt.hist(est_ploidies[\"median_pl\"],bins=30)\n", |
|
|
3669 |
"plt.title(\"est. median ploidy\")\n", |
|
|
3670 |
"\n", |
|
|
3671 |
"tmp = df_ploidies.plot.scatter(x = \"est. avg. ploidy from CN profile\",y=\"PICNIC avg. pl.\")" |
|
|
3672 |
] |
|
|
3673 |
}, |
|
|
3674 |
{ |
|
|
3675 |
"cell_type": "code", |
|
|
3676 |
"execution_count": 20, |
|
|
3677 |
"metadata": {}, |
|
|
3678 |
"outputs": [ |
|
|
3679 |
{ |
|
|
3680 |
"data": { |
|
|
3681 |
"image/png": 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\n", |
|
|
3682 |
"text/plain": [ |
|
|
3683 |
"<Figure size 432x288 with 1 Axes>" |
|
|
3684 |
] |
|
|
3685 |
}, |
|
|
3686 |
"metadata": {}, |
|
|
3687 |
"output_type": "display_data" |
|
|
3688 |
} |
|
|
3689 |
], |
|
|
3690 |
"source": [ |
|
|
3691 |
"# PICNIC average ploidy vs estimated copy-neutral \n", |
|
|
3692 |
"tmp = df_ploidies.boxplot(column=\"PICNIC avg. pl.\", by = \"est. median. ploidy\" )" |
|
|
3693 |
] |
|
|
3694 |
}, |
|
|
3695 |
{ |
|
|
3696 |
"cell_type": "markdown", |
|
|
3697 |
"metadata": {}, |
|
|
3698 |
"source": [ |
|
|
3699 |
"### Convert gene-level integer CN into log2R-like format in order to make it compatible with TCGA and CCLE\n", |
|
|
3700 |
"\n", |
|
|
3701 |
"1) Copy-neutral state was defined from average ploiy, as median of integer CN values in non-disrupted genes.\n", |
|
|
3702 |
"\n", |
|
|
3703 |
"2) Compute log2(CN/neutral-CN) for min and max CN; keep the value with most extreme estimate\n", |
|
|
3704 |
"\n", |
|
|
3705 |
"3) Replace estimates below thresholds with zeroes. " |
|
|
3706 |
] |
|
|
3707 |
}, |
|
|
3708 |
{ |
|
|
3709 |
"cell_type": "code", |
|
|
3710 |
"execution_count": 21, |
|
|
3711 |
"metadata": {}, |
|
|
3712 |
"outputs": [ |
|
|
3713 |
{ |
|
|
3714 |
"data": { |
|
|
3715 |
"text/plain": [ |
|
|
3716 |
"3.0" |
|
|
3717 |
] |
|
|
3718 |
}, |
|
|
3719 |
"execution_count": 21, |
|
|
3720 |
"metadata": {}, |
|
|
3721 |
"output_type": "execute_result" |
|
|
3722 |
} |
|
|
3723 |
], |
|
|
3724 |
"source": [ |
|
|
3725 |
"estimated_CN = est_ploidies[\"median_pl\"].to_dict()\n", |
|
|
3726 |
"estimated_CN[1287381]" |
|
|
3727 |
] |
|
|
3728 |
}, |
|
|
3729 |
{ |
|
|
3730 |
"cell_type": "code", |
|
|
3731 |
"execution_count": null, |
|
|
3732 |
"metadata": {}, |
|
|
3733 |
"outputs": [], |
|
|
3734 |
"source": [] |
|
|
3735 |
}, |
|
|
3736 |
{ |
|
|
3737 |
"cell_type": "code", |
|
|
3738 |
"execution_count": 22, |
|
|
3739 |
"metadata": {}, |
|
|
3740 |
"outputs": [ |
|
|
3741 |
{ |
|
|
3742 |
"data": { |
|
|
3743 |
"text/html": [ |
|
|
3744 |
"<div>\n", |
|
|
3745 |
"<style scoped>\n", |
|
|
3746 |
" .dataframe tbody tr th:only-of-type {\n", |
|
|
3747 |
" vertical-align: middle;\n", |
|
|
3748 |
" }\n", |
|
|
3749 |
"\n", |
|
|
3750 |
" .dataframe tbody tr th {\n", |
|
|
3751 |
" vertical-align: top;\n", |
|
|
3752 |
" }\n", |
|
|
3753 |
"\n", |
|
|
3754 |
" .dataframe thead th {\n", |
|
|
3755 |
" text-align: right;\n", |
|
|
3756 |
" }\n", |
|
|
3757 |
"</style>\n", |
|
|
3758 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
3759 |
" <thead>\n", |
|
|
3760 |
" <tr style=\"text-align: right;\">\n", |
|
|
3761 |
" <th></th>\n", |
|
|
3762 |
" <th>1287381</th>\n", |
|
|
3763 |
" <th>924100</th>\n", |
|
|
3764 |
" <th>910924</th>\n", |
|
|
3765 |
" <th>687561</th>\n", |
|
|
3766 |
" <th>1287706</th>\n", |
|
|
3767 |
" <th>687452</th>\n", |
|
|
3768 |
" <th>906798</th>\n", |
|
|
3769 |
" <th>906797</th>\n", |
|
|
3770 |
" <th>906800</th>\n", |
|
|
3771 |
" <th>910922</th>\n", |
|
|
3772 |
" <th>...</th>\n", |
|
|
3773 |
" <th>909785</th>\n", |
|
|
3774 |
" <th>909904</th>\n", |
|
|
3775 |
" <th>909905</th>\n", |
|
|
3776 |
" <th>687592</th>\n", |
|
|
3777 |
" <th>1303911</th>\n", |
|
|
3778 |
" <th>946358</th>\n", |
|
|
3779 |
" <th>909907</th>\n", |
|
|
3780 |
" <th>1298146</th>\n", |
|
|
3781 |
" <th>908452</th>\n", |
|
|
3782 |
" <th>908450</th>\n", |
|
|
3783 |
" </tr>\n", |
|
|
3784 |
" </thead>\n", |
|
|
3785 |
" <tbody>\n", |
|
|
3786 |
" <tr>\n", |
|
|
3787 |
" <th>5S_rRNA</th>\n", |
|
|
3788 |
" <td>-4.320000</td>\n", |
|
|
3789 |
" <td>1.807355</td>\n", |
|
|
3790 |
" <td>2.0</td>\n", |
|
|
3791 |
" <td>-0.415037</td>\n", |
|
|
3792 |
" <td>-4.32</td>\n", |
|
|
3793 |
" <td>-4.320000</td>\n", |
|
|
3794 |
" <td>-1.00</td>\n", |
|
|
3795 |
" <td>2.807355</td>\n", |
|
|
3796 |
" <td>2.169925</td>\n", |
|
|
3797 |
" <td>-1.00</td>\n", |
|
|
3798 |
" <td>...</td>\n", |
|
|
3799 |
" <td>-4.32</td>\n", |
|
|
3800 |
" <td>2.222392</td>\n", |
|
|
3801 |
" <td>-4.32</td>\n", |
|
|
3802 |
" <td>-4.320000</td>\n", |
|
|
3803 |
" <td>-4.32</td>\n", |
|
|
3804 |
" <td>1.807355</td>\n", |
|
|
3805 |
" <td>-4.320000</td>\n", |
|
|
3806 |
" <td>1.736966</td>\n", |
|
|
3807 |
" <td>2.169925</td>\n", |
|
|
3808 |
" <td>-1.584963</td>\n", |
|
|
3809 |
" </tr>\n", |
|
|
3810 |
" <tr>\n", |
|
|
3811 |
" <th>5_8S_rRNA</th>\n", |
|
|
3812 |
" <td>-0.584963</td>\n", |
|
|
3813 |
" <td>0.000000</td>\n", |
|
|
3814 |
" <td>0.0</td>\n", |
|
|
3815 |
" <td>-0.415037</td>\n", |
|
|
3816 |
" <td>0.00</td>\n", |
|
|
3817 |
" <td>-0.584963</td>\n", |
|
|
3818 |
" <td>0.00</td>\n", |
|
|
3819 |
" <td>0.000000</td>\n", |
|
|
3820 |
" <td>0.000000</td>\n", |
|
|
3821 |
" <td>0.00</td>\n", |
|
|
3822 |
" <td>...</td>\n", |
|
|
3823 |
" <td>0.00</td>\n", |
|
|
3824 |
" <td>0.415037</td>\n", |
|
|
3825 |
" <td>0.00</td>\n", |
|
|
3826 |
" <td>-0.584963</td>\n", |
|
|
3827 |
" <td>-4.32</td>\n", |
|
|
3828 |
" <td>0.000000</td>\n", |
|
|
3829 |
" <td>-0.415037</td>\n", |
|
|
3830 |
" <td>0.000000</td>\n", |
|
|
3831 |
" <td>0.000000</td>\n", |
|
|
3832 |
" <td>-0.584963</td>\n", |
|
|
3833 |
" </tr>\n", |
|
|
3834 |
" <tr>\n", |
|
|
3835 |
" <th>7SK</th>\n", |
|
|
3836 |
" <td>1.000000</td>\n", |
|
|
3837 |
" <td>0.000000</td>\n", |
|
|
3838 |
" <td>0.0</td>\n", |
|
|
3839 |
" <td>-4.320000</td>\n", |
|
|
3840 |
" <td>-4.32</td>\n", |
|
|
3841 |
" <td>-0.584963</td>\n", |
|
|
3842 |
" <td>-4.32</td>\n", |
|
|
3843 |
" <td>0.584963</td>\n", |
|
|
3844 |
" <td>0.000000</td>\n", |
|
|
3845 |
" <td>-4.32</td>\n", |
|
|
3846 |
" <td>...</td>\n", |
|
|
3847 |
" <td>-4.32</td>\n", |
|
|
3848 |
" <td>0.000000</td>\n", |
|
|
3849 |
" <td>-4.32</td>\n", |
|
|
3850 |
" <td>-4.320000</td>\n", |
|
|
3851 |
" <td>-4.32</td>\n", |
|
|
3852 |
" <td>-0.415037</td>\n", |
|
|
3853 |
" <td>-4.320000</td>\n", |
|
|
3854 |
" <td>-4.320000</td>\n", |
|
|
3855 |
" <td>0.000000</td>\n", |
|
|
3856 |
" <td>-4.320000</td>\n", |
|
|
3857 |
" </tr>\n", |
|
|
3858 |
" </tbody>\n", |
|
|
3859 |
"</table>\n", |
|
|
3860 |
"<p>3 rows × 996 columns</p>\n", |
|
|
3861 |
"</div>" |
|
|
3862 |
], |
|
|
3863 |
"text/plain": [ |
|
|
3864 |
" 1287381 924100 910924 687561 1287706 687452 906798 \\\n", |
|
|
3865 |
"5S_rRNA -4.320000 1.807355 2.0 -0.415037 -4.32 -4.320000 -1.00 \n", |
|
|
3866 |
"5_8S_rRNA -0.584963 0.000000 0.0 -0.415037 0.00 -0.584963 0.00 \n", |
|
|
3867 |
"7SK 1.000000 0.000000 0.0 -4.320000 -4.32 -0.584963 -4.32 \n", |
|
|
3868 |
"\n", |
|
|
3869 |
" 906797 906800 910922 ... 909785 909904 909905 \\\n", |
|
|
3870 |
"5S_rRNA 2.807355 2.169925 -1.00 ... -4.32 2.222392 -4.32 \n", |
|
|
3871 |
"5_8S_rRNA 0.000000 0.000000 0.00 ... 0.00 0.415037 0.00 \n", |
|
|
3872 |
"7SK 0.584963 0.000000 -4.32 ... -4.32 0.000000 -4.32 \n", |
|
|
3873 |
"\n", |
|
|
3874 |
" 687592 1303911 946358 909907 1298146 908452 908450 \n", |
|
|
3875 |
"5S_rRNA -4.320000 -4.32 1.807355 -4.320000 1.736966 2.169925 -1.584963 \n", |
|
|
3876 |
"5_8S_rRNA -0.584963 -4.32 0.000000 -0.415037 0.000000 0.000000 -0.584963 \n", |
|
|
3877 |
"7SK -4.320000 -4.32 -0.415037 -4.320000 -4.320000 0.000000 -4.320000 \n", |
|
|
3878 |
"\n", |
|
|
3879 |
"[3 rows x 996 columns]" |
|
|
3880 |
] |
|
|
3881 |
}, |
|
|
3882 |
"execution_count": 22, |
|
|
3883 |
"metadata": {}, |
|
|
3884 |
"output_type": "execute_result" |
|
|
3885 |
} |
|
|
3886 |
], |
|
|
3887 |
"source": [ |
|
|
3888 |
"gdsc = gdsc.apply(lambda x : CN2log2R(x,estimated_CN[x.name] ))\n", |
|
|
3889 |
"# drop genes without any determined value\n", |
|
|
3890 |
"gdsc = gdsc.dropna(axis=0,how=\"all\")\n", |
|
|
3891 |
"# fill with zeroes the remaining ones\n", |
|
|
3892 |
"gdsc.fillna(0,inplace=True)\n", |
|
|
3893 |
"gdsc.head(3)" |
|
|
3894 |
] |
|
|
3895 |
}, |
|
|
3896 |
{ |
|
|
3897 |
"cell_type": "code", |
|
|
3898 |
"execution_count": 23, |
|
|
3899 |
"metadata": {}, |
|
|
3900 |
"outputs": [], |
|
|
3901 |
"source": [ |
|
|
3902 |
"\n", |
|
|
3903 |
"gdsc = gdsc.applymap(lambda x : clean_logR(x, pos_seg_mean_thr, neg_seg_mean_thr))" |
|
|
3904 |
] |
|
|
3905 |
}, |
|
|
3906 |
{ |
|
|
3907 |
"cell_type": "code", |
|
|
3908 |
"execution_count": 24, |
|
|
3909 |
"metadata": {}, |
|
|
3910 |
"outputs": [ |
|
|
3911 |
{ |
|
|
3912 |
"name": "stderr", |
|
|
3913 |
"output_type": "stream", |
|
|
3914 |
"text": [ |
|
|
3915 |
"Ok: no empty rows detected\n", |
|
|
3916 |
"Ok: no duplicated pairs detected\n", |
|
|
3917 |
"Ok: All Symbol rows are not empty.\n", |
|
|
3918 |
"Ok: All Symbol are mapped to GeneID\n", |
|
|
3919 |
"16 Symbol mapped to multiple GeneID\n", |
|
|
3920 |
"Ok: All GeneID are unique\n", |
|
|
3921 |
"59266 Symbol can be mapped directly to GeneID\n" |
|
|
3922 |
] |
|
|
3923 |
} |
|
|
3924 |
], |
|
|
3925 |
"source": [ |
|
|
3926 |
"NCBI = pd.read_csv(root_dir+\"Homo_sapiens.gene_info\",sep = \"\\t\")\n", |
|
|
3927 |
"NCBI = NCBI[[\"#tax_id\",\"GeneID\",\"Symbol\",\"Synonyms\",\"type_of_gene\"]]\n", |
|
|
3928 |
"NCBI = NCBI.loc[NCBI[\"#tax_id\"] == 9606]\n", |
|
|
3929 |
"NCBI = NCBI.loc[NCBI[\"type_of_gene\"] != \"unknown\"]\n", |
|
|
3930 |
"ncbi_symbols = parse_mapping_table(NCBI, \"Symbol\",\"GeneID\")" |
|
|
3931 |
] |
|
|
3932 |
}, |
|
|
3933 |
{ |
|
|
3934 |
"cell_type": "code", |
|
|
3935 |
"execution_count": 25, |
|
|
3936 |
"metadata": {}, |
|
|
3937 |
"outputs": [ |
|
|
3938 |
{ |
|
|
3939 |
"name": "stderr", |
|
|
3940 |
"output_type": "stream", |
|
|
3941 |
"text": [ |
|
|
3942 |
"Ok: no empty rows detected\n", |
|
|
3943 |
"Ok: no duplicated pairs detected\n", |
|
|
3944 |
"Ok: All Synonyms rows are not empty.\n", |
|
|
3945 |
"Ok: All Synonyms are mapped to GeneID\n", |
|
|
3946 |
"3145 Synonyms mapped to multiple GeneID\n", |
|
|
3947 |
"49179 different Synonyms mapped to the same GeneID\n", |
|
|
3948 |
"10839 Synonyms can be mapped directly to GeneID\n" |
|
|
3949 |
] |
|
|
3950 |
} |
|
|
3951 |
], |
|
|
3952 |
"source": [ |
|
|
3953 |
"ncbi_synonyms = expand(NCBI[[\"Synonyms\",\"GeneID\"]],column=\"Synonyms\",sep=\"|\") \n", |
|
|
3954 |
"ncbi_synonyms = parse_mapping_table(ncbi_synonyms, \"Synonyms\",\"GeneID\")" |
|
|
3955 |
] |
|
|
3956 |
}, |
|
|
3957 |
{ |
|
|
3958 |
"cell_type": "code", |
|
|
3959 |
"execution_count": 26, |
|
|
3960 |
"metadata": {}, |
|
|
3961 |
"outputs": [ |
|
|
3962 |
{ |
|
|
3963 |
"name": "stdout", |
|
|
3964 |
"output_type": "stream", |
|
|
3965 |
"text": [ |
|
|
3966 |
"Mapped: 24545 \n", |
|
|
3967 |
"\tdirectly via main_mapper 22363 \n", |
|
|
3968 |
"\tvia alternative mapper 766 \n", |
|
|
3969 |
"\tvia one of multiple synonyms in alternative mapper 1416 \n", |
|
|
3970 |
"\tLOC 0 \n", |
|
|
3971 |
"Unmapped: 21587 \n", |
|
|
3972 |
"\trecognized symbols without Entrez ID 0 \n", |
|
|
3973 |
"\tmultiple query_ids map to the same target_id 0 \n", |
|
|
3974 |
"\tquery_ids map to multiple target_ids in the main mapper 0 \n", |
|
|
3975 |
"\tquery_ids map to multiple target_ids in the alternative mapper 76 \n", |
|
|
3976 |
"\tLOC not found in Entrez 0 \n", |
|
|
3977 |
"\tNot found at all: 21511\n", |
|
|
3978 |
"Warning: query IDs mapping to duplicated target IDs in mapping table: 156\n", |
|
|
3979 |
"Warning: query IDs not mapped to any target IDs excluded: 21587\n" |
|
|
3980 |
] |
|
|
3981 |
}, |
|
|
3982 |
{ |
|
|
3983 |
"name": "stderr", |
|
|
3984 |
"output_type": "stream", |
|
|
3985 |
"text": [ |
|
|
3986 |
"/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/frame.py:3781: SettingWithCopyWarning: \n", |
|
|
3987 |
"A value is trying to be set on a copy of a slice from a DataFrame\n", |
|
|
3988 |
"\n", |
|
|
3989 |
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", |
|
|
3990 |
" return super(DataFrame, self).rename(**kwargs)\n", |
|
|
3991 |
"IDs mapped to multiple target IDs are kept:\n", |
|
|
3992 |
" [143872, 286464, 140290, 414212, 414213, 51463, 642826, 84631, 574445, 399761, 100132115, 647060, 284565, 6551, 161176, 341019, 4253, 9502, 442416, 51236, 643749, 54438, 728113, 100302179, 414761, 29099, 729438, 256815, 10160, 645425, 653234, 644019, 26165, 3255, 644509, 2749, 653505, 653067, 643479, 100462820, 100418977, 26824, 79817, 6218, 728695, 100034743, 221262, 647507, 677844, 728917, 26583, 100289124, 84316, 200030, 768096, 642658, 23523, 401508, 23334, 119016, 106478953, 84458, 1517, 246126, 26095, 100033392, 92017, 374, 26871, 100132948, 125050, 387707, 653308, 79741, 728798]\n", |
|
|
3993 |
"mapper.py:204: SettingWithCopyWarning: \n", |
|
|
3994 |
"A value is trying to be set on a copy of a slice from a DataFrame\n", |
|
|
3995 |
"\n", |
|
|
3996 |
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", |
|
|
3997 |
" df.sort_index(inplace=True)\n" |
|
|
3998 |
] |
|
|
3999 |
}, |
|
|
4000 |
{ |
|
|
4001 |
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4007 |
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4010 |
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4018 |
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4019 |
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|
4020 |
" <th></th>\n", |
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|
4021 |
" <th>1287381</th>\n", |
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4022 |
" <th>924100</th>\n", |
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4023 |
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4024 |
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4025 |
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4026 |
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4027 |
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4028 |
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4029 |
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|
4030 |
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|
4031 |
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|
4032 |
" <th>909785</th>\n", |
|
|
4033 |
" <th>909904</th>\n", |
|
|
4034 |
" <th>909905</th>\n", |
|
|
4035 |
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4036 |
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|
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4037 |
" <th>946358</th>\n", |
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4038 |
" <th>909907</th>\n", |
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4039 |
" <th>1298146</th>\n", |
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4040 |
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4041 |
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4043 |
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4044 |
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|
|
4045 |
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|
|
4046 |
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|
|
4047 |
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4048 |
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4049 |
" <td>0.0</td>\n", |
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4050 |
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4051 |
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4052 |
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4053 |
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4054 |
" <td>0.584963</td>\n", |
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4055 |
" <td>0.0</td>\n", |
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4056 |
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4057 |
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4058 |
" <td>0.0</td>\n", |
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4059 |
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4060 |
" <td>0.584963</td>\n", |
|
|
4061 |
" <td>0.415037</td>\n", |
|
|
4062 |
" <td>0.000000</td>\n", |
|
|
4063 |
" <td>0.000000</td>\n", |
|
|
4064 |
" <td>0.0</td>\n", |
|
|
4065 |
" <td>0.000000</td>\n", |
|
|
4066 |
" <td>0.584963</td>\n", |
|
|
4067 |
" <td>0.415037</td>\n", |
|
|
4068 |
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|
|
4069 |
" <tr>\n", |
|
|
4070 |
" <th>2</th>\n", |
|
|
4071 |
" <td>0.000000</td>\n", |
|
|
4072 |
" <td>0.584963</td>\n", |
|
|
4073 |
" <td>0.0</td>\n", |
|
|
4074 |
" <td>-0.415037</td>\n", |
|
|
4075 |
" <td>0.321928</td>\n", |
|
|
4076 |
" <td>0.000000</td>\n", |
|
|
4077 |
" <td>0.584963</td>\n", |
|
|
4078 |
" <td>0.584963</td>\n", |
|
|
4079 |
" <td>0.0</td>\n", |
|
|
4080 |
" <td>0.0</td>\n", |
|
|
4081 |
" <td>...</td>\n", |
|
|
4082 |
" <td>0.0</td>\n", |
|
|
4083 |
" <td>-0.584963</td>\n", |
|
|
4084 |
" <td>0.000000</td>\n", |
|
|
4085 |
" <td>0.000000</td>\n", |
|
|
4086 |
" <td>0.736966</td>\n", |
|
|
4087 |
" <td>0.321928</td>\n", |
|
|
4088 |
" <td>0.0</td>\n", |
|
|
4089 |
" <td>-0.584963</td>\n", |
|
|
4090 |
" <td>0.000000</td>\n", |
|
|
4091 |
" <td>0.736966</td>\n", |
|
|
4092 |
" </tr>\n", |
|
|
4093 |
" <tr>\n", |
|
|
4094 |
" <th>9</th>\n", |
|
|
4095 |
" <td>-0.584963</td>\n", |
|
|
4096 |
" <td>0.584963</td>\n", |
|
|
4097 |
" <td>0.0</td>\n", |
|
|
4098 |
" <td>-0.415037</td>\n", |
|
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4099 |
" <td>-0.415037</td>\n", |
|
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4100 |
" <td>-0.584963</td>\n", |
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4101 |
" <td>0.000000</td>\n", |
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4102 |
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4103 |
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4104 |
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4106 |
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4107 |
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4108 |
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4109 |
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4110 |
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4117 |
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|
|
4118 |
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|
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4119 |
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4125 |
"2 0.000000 0.584963 0.0 -0.415037 0.321928 0.000000 0.584963 \n", |
|
|
4126 |
"9 -0.584963 0.584963 0.0 -0.415037 -0.415037 -0.584963 0.000000 \n", |
|
|
4127 |
"\n", |
|
|
4128 |
" 906797 906800 910922 ... 909785 909904 909905 \\\n", |
|
|
4129 |
"1 0.584963 0.0 0.0 ... 0.0 -0.584963 0.584963 \n", |
|
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4130 |
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|
|
4131 |
"9 0.000000 0.0 0.0 ... 0.0 -0.584963 0.000000 \n", |
|
|
4132 |
"\n", |
|
|
4133 |
" 687592 1303911 946358 909907 1298146 908452 908450 \n", |
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4134 |
"1 0.415037 0.000000 0.000000 0.0 0.000000 0.584963 0.415037 \n", |
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"2 0.000000 0.736966 0.321928 0.0 -0.584963 0.000000 0.736966 \n", |
|
|
4136 |
"9 0.415037 0.000000 0.000000 -1.0 -0.584963 0.000000 0.000000 \n", |
|
|
4137 |
"\n", |
|
|
4138 |
"[3 rows x 996 columns]" |
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|
4139 |
] |
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|
4140 |
}, |
|
|
4141 |
"execution_count": 26, |
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|
4142 |
"metadata": {}, |
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"output_type": "execute_result" |
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} |
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4147 |
"gdsc,query2target,not_mapped = apply_mappers(gdsc, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"keep\")\n", |
|
|
4148 |
"gdsc.head(3)" |
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4150 |
}, |
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4151 |
{ |
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4152 |
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4161 |
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4162 |
"75 duplicated IDs in 156 rows found.\n", |
|
|
4163 |
"duplicate rows removed due to low correlation of duplicated profiles 25\n", |
|
|
4164 |
"Merged 131 duplicated rows into 63 rows\n" |
|
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4165 |
] |
|
|
4166 |
} |
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4167 |
], |
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4168 |
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4264 |
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4271 |
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|
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|
4295 |
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4297 |
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4298 |
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4299 |
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4300 |
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4301 |
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4302 |
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4303 |
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4304 |
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|
4305 |
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|
4306 |
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|
4307 |
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4308 |
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4309 |
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|
4310 |
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|
4311 |
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|
4312 |
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|
4313 |
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4314 |
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4315 |
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|
4316 |
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|
4317 |
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4318 |
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|
4319 |
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4320 |
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4321 |
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4322 |
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4323 |
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4324 |
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4325 |
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4326 |
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4327 |
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4328 |
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4329 |
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4330 |
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4331 |
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4332 |
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4333 |
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4334 |
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4335 |
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4336 |
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4337 |
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4338 |
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4339 |
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4340 |
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|
4341 |
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|
4342 |
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|
4343 |
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4344 |
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4345 |
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4346 |
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4347 |
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4348 |
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4349 |
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4350 |
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4351 |
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4352 |
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4353 |
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4354 |
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4355 |
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|
4356 |
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|
4357 |
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4358 |
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4359 |
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4360 |
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4361 |
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4362 |
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|
4363 |
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|
|
4364 |
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|
4365 |
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|
4366 |
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|
4367 |
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|
|
4368 |
"<p>5 rows × 996 columns</p>\n", |
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|
4369 |
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4370 |
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4371 |
"text/plain": [ |
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4372 |
" 683665 683667 684052 684055 684057 684059 684062 \\\n", |
|
|
4373 |
"gene_id \n", |
|
|
4374 |
"1 0.0 0.000000 0.0 0.000000 -0.415037 0.0 -0.415037 \n", |
|
|
4375 |
"2 0.0 0.000000 0.0 0.584963 0.000000 0.0 0.000000 \n", |
|
|
4376 |
"9 0.0 0.321928 0.0 0.584963 0.584963 0.0 0.321928 \n", |
|
|
4377 |
"10 0.0 0.321928 0.0 0.584963 0.584963 0.0 0.321928 \n", |
|
|
4378 |
"12 0.0 -1.000000 0.0 0.000000 -1.000000 0.0 -0.415037 \n", |
|
|
4379 |
"\n", |
|
|
4380 |
" 684072 684681 687448 ... 1659818 1659819 1659823 \\\n", |
|
|
4381 |
"gene_id ... \n", |
|
|
4382 |
"1 0.000000 0.415037 0.0 ... 0.0 0.0 0.000000 \n", |
|
|
4383 |
"2 0.584963 0.000000 0.0 ... 0.0 0.0 0.000000 \n", |
|
|
4384 |
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|
|
4385 |
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|
|
4386 |
"12 0.000000 0.000000 0.0 ... -1.0 0.0 0.321928 \n", |
|
|
4387 |
"\n", |
|
|
4388 |
" 1659928 1659929 1660034 1660035 1660036 1674021 1789883 \n", |
|
|
4389 |
"gene_id \n", |
|
|
4390 |
"1 0.0 -0.415037 0.0 -0.584963 0.000000 0.000000 0.321928 \n", |
|
|
4391 |
"2 0.0 0.000000 0.0 0.000000 0.000000 0.584963 -0.415037 \n", |
|
|
4392 |
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|
|
4393 |
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|
|
4394 |
"12 0.0 -0.415037 0.0 0.415037 0.584963 0.000000 0.000000 \n", |
|
|
4395 |
"\n", |
|
|
4396 |
"[5 rows x 996 columns]" |
|
|
4397 |
] |
|
|
4398 |
}, |
|
|
4399 |
"execution_count": 28, |
|
|
4400 |
"metadata": {}, |
|
|
4401 |
"output_type": "execute_result" |
|
|
4402 |
} |
|
|
4403 |
], |
|
|
4404 |
"source": [ |
|
|
4405 |
"gdsc.index.name = \"gene_id\"\n", |
|
|
4406 |
"gdsc = gdsc.T.sort_index().T\n", |
|
|
4407 |
"gdsc.head()" |
|
|
4408 |
] |
|
|
4409 |
}, |
|
|
4410 |
{ |
|
|
4411 |
"cell_type": "code", |
|
|
4412 |
"execution_count": 29, |
|
|
4413 |
"metadata": {}, |
|
|
4414 |
"outputs": [], |
|
|
4415 |
"source": [ |
|
|
4416 |
"gdsc.to_csv(preprocessed_dir+\"/\"+\"GDSC\"+\".Segment_Mean.CNA.tsv\",\n", |
|
|
4417 |
" sep = \"\\t\",header=True,index=True)" |
|
|
4418 |
] |
|
|
4419 |
}, |
|
|
4420 |
{ |
|
|
4421 |
"cell_type": "markdown", |
|
|
4422 |
"metadata": {}, |
|
|
4423 |
"source": [ |
|
|
4424 |
"# PDX \n", |
|
|
4425 |
"\n", |
|
|
4426 |
"For PDX dataset only gene-level estimated copy-number (non-integer) reported. \n", |
|
|
4427 |
"From ploidy distributions, calculated as average over all genes we concluded that CN estimates were called under assumption that copy-neutral state of each xenograft corresponds CN = 2.\n", |
|
|
4428 |
"\n", |
|
|
4429 |
"\n", |
|
|
4430 |
"For gene ID conversion we used the same approach as for RNA-seq." |
|
|
4431 |
] |
|
|
4432 |
}, |
|
|
4433 |
{ |
|
|
4434 |
"cell_type": "code", |
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|
4435 |
"execution_count": 30, |
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|
4436 |
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|
4437 |
"outputs": [ |
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4438 |
{ |
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4439 |
"name": "stdout", |
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4440 |
"output_type": "stream", |
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4441 |
"text": [ |
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|
4442 |
"(23852, 375)\n" |
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|
4443 |
] |
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4446 |
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4451 |
" vertical-align: middle;\n", |
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4452 |
" }\n", |
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4453 |
"\n", |
|
|
4454 |
" .dataframe tbody tr th {\n", |
|
|
4455 |
" vertical-align: top;\n", |
|
|
4456 |
" }\n", |
|
|
4457 |
"\n", |
|
|
4458 |
" .dataframe thead th {\n", |
|
|
4459 |
" text-align: right;\n", |
|
|
4460 |
" }\n", |
|
|
4461 |
"</style>\n", |
|
|
4462 |
"<table border=\"1\" class=\"dataframe\">\n", |
|
|
4463 |
" <thead>\n", |
|
|
4464 |
" <tr style=\"text-align: right;\">\n", |
|
|
4465 |
" <th></th>\n", |
|
|
4466 |
" <th>X-1004</th>\n", |
|
|
4467 |
" <th>X-1008</th>\n", |
|
|
4468 |
" <th>X-1027</th>\n", |
|
|
4469 |
" <th>X-1095</th>\n", |
|
|
4470 |
" <th>X-1119</th>\n", |
|
|
4471 |
" <th>X-1156</th>\n", |
|
|
4472 |
" <th>X-1167</th>\n", |
|
|
4473 |
" <th>X-1169</th>\n", |
|
|
4474 |
" <th>X-1172</th>\n", |
|
|
4475 |
" <th>X-1173</th>\n", |
|
|
4476 |
" <th>...</th>\n", |
|
|
4477 |
" <th>X-5694</th>\n", |
|
|
4478 |
" <th>X-5696</th>\n", |
|
|
4479 |
" <th>X-5713</th>\n", |
|
|
4480 |
" <th>X-5717</th>\n", |
|
|
4481 |
" <th>X-5727</th>\n", |
|
|
4482 |
" <th>X-5739</th>\n", |
|
|
4483 |
" <th>X-5808</th>\n", |
|
|
4484 |
" <th>X-5959</th>\n", |
|
|
4485 |
" <th>X-5975</th>\n", |
|
|
4486 |
" <th>X-6047</th>\n", |
|
|
4487 |
" </tr>\n", |
|
|
4488 |
" <tr>\n", |
|
|
4489 |
" <th>Sample</th>\n", |
|
|
4490 |
" <th></th>\n", |
|
|
4491 |
" <th></th>\n", |
|
|
4492 |
" <th></th>\n", |
|
|
4493 |
" <th></th>\n", |
|
|
4494 |
" <th></th>\n", |
|
|
4495 |
" <th></th>\n", |
|
|
4496 |
" <th></th>\n", |
|
|
4497 |
" <th></th>\n", |
|
|
4498 |
" <th></th>\n", |
|
|
4499 |
" <th></th>\n", |
|
|
4500 |
" <th></th>\n", |
|
|
4501 |
" <th></th>\n", |
|
|
4502 |
" <th></th>\n", |
|
|
4503 |
" <th></th>\n", |
|
|
4504 |
" <th></th>\n", |
|
|
4505 |
" <th></th>\n", |
|
|
4506 |
" <th></th>\n", |
|
|
4507 |
" <th></th>\n", |
|
|
4508 |
" <th></th>\n", |
|
|
4509 |
" <th></th>\n", |
|
|
4510 |
" <th></th>\n", |
|
|
4511 |
" </tr>\n", |
|
|
4512 |
" </thead>\n", |
|
|
4513 |
" <tbody>\n", |
|
|
4514 |
" <tr>\n", |
|
|
4515 |
" <th>A1BG</th>\n", |
|
|
4516 |
" <td>2.58</td>\n", |
|
|
4517 |
" <td>1.60</td>\n", |
|
|
4518 |
" <td>2.17</td>\n", |
|
|
4519 |
" <td>2.08</td>\n", |
|
|
4520 |
" <td>2.00</td>\n", |
|
|
4521 |
" <td>3.94</td>\n", |
|
|
4522 |
" <td>2.04</td>\n", |
|
|
4523 |
" <td>11.39</td>\n", |
|
|
4524 |
" <td>2.17</td>\n", |
|
|
4525 |
" <td>2.01</td>\n", |
|
|
4526 |
" <td>...</td>\n", |
|
|
4527 |
" <td>2.08</td>\n", |
|
|
4528 |
" <td>2.10</td>\n", |
|
|
4529 |
" <td>2.14</td>\n", |
|
|
4530 |
" <td>2.95</td>\n", |
|
|
4531 |
" <td>2.06</td>\n", |
|
|
4532 |
" <td>2.07</td>\n", |
|
|
4533 |
" <td>1.99</td>\n", |
|
|
4534 |
" <td>2.07</td>\n", |
|
|
4535 |
" <td>1.43</td>\n", |
|
|
4536 |
" <td>2.03</td>\n", |
|
|
4537 |
" </tr>\n", |
|
|
4538 |
" <tr>\n", |
|
|
4539 |
" <th>A1BG-AS1</th>\n", |
|
|
4540 |
" <td>2.58</td>\n", |
|
|
4541 |
" <td>1.60</td>\n", |
|
|
4542 |
" <td>2.17</td>\n", |
|
|
4543 |
" <td>2.08</td>\n", |
|
|
4544 |
" <td>2.00</td>\n", |
|
|
4545 |
" <td>3.94</td>\n", |
|
|
4546 |
" <td>2.04</td>\n", |
|
|
4547 |
" <td>11.39</td>\n", |
|
|
4548 |
" <td>2.17</td>\n", |
|
|
4549 |
" <td>2.01</td>\n", |
|
|
4550 |
" <td>...</td>\n", |
|
|
4551 |
" <td>2.08</td>\n", |
|
|
4552 |
" <td>2.10</td>\n", |
|
|
4553 |
" <td>2.14</td>\n", |
|
|
4554 |
" <td>2.95</td>\n", |
|
|
4555 |
" <td>2.06</td>\n", |
|
|
4556 |
" <td>2.07</td>\n", |
|
|
4557 |
" <td>1.99</td>\n", |
|
|
4558 |
" <td>2.07</td>\n", |
|
|
4559 |
" <td>1.43</td>\n", |
|
|
4560 |
" <td>2.03</td>\n", |
|
|
4561 |
" </tr>\n", |
|
|
4562 |
" <tr>\n", |
|
|
4563 |
" <th>A1CF</th>\n", |
|
|
4564 |
" <td>2.87</td>\n", |
|
|
4565 |
" <td>2.97</td>\n", |
|
|
4566 |
" <td>2.01</td>\n", |
|
|
4567 |
" <td>2.06</td>\n", |
|
|
4568 |
" <td>2.10</td>\n", |
|
|
4569 |
" <td>1.58</td>\n", |
|
|
4570 |
" <td>2.01</td>\n", |
|
|
4571 |
" <td>1.64</td>\n", |
|
|
4572 |
" <td>1.89</td>\n", |
|
|
4573 |
" <td>1.99</td>\n", |
|
|
4574 |
" <td>...</td>\n", |
|
|
4575 |
" <td>2.04</td>\n", |
|
|
4576 |
" <td>0.97</td>\n", |
|
|
4577 |
" <td>1.58</td>\n", |
|
|
4578 |
" <td>2.08</td>\n", |
|
|
4579 |
" <td>1.95</td>\n", |
|
|
4580 |
" <td>1.92</td>\n", |
|
|
4581 |
" <td>1.54</td>\n", |
|
|
4582 |
" <td>1.28</td>\n", |
|
|
4583 |
" <td>1.33</td>\n", |
|
|
4584 |
" <td>2.10</td>\n", |
|
|
4585 |
" </tr>\n", |
|
|
4586 |
" <tr>\n", |
|
|
4587 |
" <th>A2LD1</th>\n", |
|
|
4588 |
" <td>5.74</td>\n", |
|
|
4589 |
" <td>1.64</td>\n", |
|
|
4590 |
" <td>2.06</td>\n", |
|
|
4591 |
" <td>2.01</td>\n", |
|
|
4592 |
" <td>2.07</td>\n", |
|
|
4593 |
" <td>1.74</td>\n", |
|
|
4594 |
" <td>2.06</td>\n", |
|
|
4595 |
" <td>1.59</td>\n", |
|
|
4596 |
" <td>1.40</td>\n", |
|
|
4597 |
" <td>2.53</td>\n", |
|
|
4598 |
" <td>...</td>\n", |
|
|
4599 |
" <td>2.03</td>\n", |
|
|
4600 |
" <td>2.07</td>\n", |
|
|
4601 |
" <td>2.25</td>\n", |
|
|
4602 |
" <td>2.00</td>\n", |
|
|
4603 |
" <td>1.01</td>\n", |
|
|
4604 |
" <td>2.00</td>\n", |
|
|
4605 |
" <td>1.08</td>\n", |
|
|
4606 |
" <td>1.85</td>\n", |
|
|
4607 |
" <td>1.93</td>\n", |
|
|
4608 |
" <td>1.45</td>\n", |
|
|
4609 |
" </tr>\n", |
|
|
4610 |
" </tbody>\n", |
|
|
4611 |
"</table>\n", |
|
|
4612 |
"<p>4 rows × 375 columns</p>\n", |
|
|
4613 |
"</div>" |
|
|
4614 |
], |
|
|
4615 |
"text/plain": [ |
|
|
4616 |
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 X-1169 \\\n", |
|
|
4617 |
"Sample \n", |
|
|
4618 |
"A1BG 2.58 1.60 2.17 2.08 2.00 3.94 2.04 11.39 \n", |
|
|
4619 |
"A1BG-AS1 2.58 1.60 2.17 2.08 2.00 3.94 2.04 11.39 \n", |
|
|
4620 |
"A1CF 2.87 2.97 2.01 2.06 2.10 1.58 2.01 1.64 \n", |
|
|
4621 |
"A2LD1 5.74 1.64 2.06 2.01 2.07 1.74 2.06 1.59 \n", |
|
|
4622 |
"\n", |
|
|
4623 |
" X-1172 X-1173 ... X-5694 X-5696 X-5713 X-5717 X-5727 \\\n", |
|
|
4624 |
"Sample ... \n", |
|
|
4625 |
"A1BG 2.17 2.01 ... 2.08 2.10 2.14 2.95 2.06 \n", |
|
|
4626 |
"A1BG-AS1 2.17 2.01 ... 2.08 2.10 2.14 2.95 2.06 \n", |
|
|
4627 |
"A1CF 1.89 1.99 ... 2.04 0.97 1.58 2.08 1.95 \n", |
|
|
4628 |
"A2LD1 1.40 2.53 ... 2.03 2.07 2.25 2.00 1.01 \n", |
|
|
4629 |
"\n", |
|
|
4630 |
" X-5739 X-5808 X-5959 X-5975 X-6047 \n", |
|
|
4631 |
"Sample \n", |
|
|
4632 |
"A1BG 2.07 1.99 2.07 1.43 2.03 \n", |
|
|
4633 |
"A1BG-AS1 2.07 1.99 2.07 1.43 2.03 \n", |
|
|
4634 |
"A1CF 1.92 1.54 1.28 1.33 2.10 \n", |
|
|
4635 |
"A2LD1 2.00 1.08 1.85 1.93 1.45 \n", |
|
|
4636 |
"\n", |
|
|
4637 |
"[4 rows x 375 columns]" |
|
|
4638 |
] |
|
|
4639 |
}, |
|
|
4640 |
"execution_count": 30, |
|
|
4641 |
"metadata": {}, |
|
|
4642 |
"output_type": "execute_result" |
|
|
4643 |
} |
|
|
4644 |
], |
|
|
4645 |
"source": [ |
|
|
4646 |
"PDX_xls = \"/home/olya/SFU/Hossein/PDX/nm.3954-S2.xlsx\"\n", |
|
|
4647 |
"pdx = pd.read_excel(PDX_xls,\"copy number\")\n", |
|
|
4648 |
"pdx.set_index(\"Sample\",drop=True,inplace=True)\n", |
|
|
4649 |
"focal = pdx.T[\"FocalCNScore\"]\n", |
|
|
4650 |
"pdx.drop([\"ArmLevelCNScore\",\"FocalCNScore\"],inplace = True)\n", |
|
|
4651 |
"print(pdx.shape)\n", |
|
|
4652 |
"pdx.head(4)" |
|
|
4653 |
] |
|
|
4654 |
}, |
|
|
4655 |
{ |
|
|
4656 |
"cell_type": "code", |
|
|
4657 |
"execution_count": 31, |
|
|
4658 |
"metadata": {}, |
|
|
4659 |
"outputs": [ |
|
|
4660 |
{ |
|
|
4661 |
"name": "stdout", |
|
|
4662 |
"output_type": "stream", |
|
|
4663 |
"text": [ |
|
|
4664 |
"Strings containing duplicated gene IDs: 544\n", |
|
|
4665 |
"268 duplicated IDs in 544 rows found.\n", |
|
|
4666 |
"duplicate rows removed due to low correlation of duplicated profiles 134\n", |
|
|
4667 |
"Merged 410 duplicated rows into 205 rows\n" |
|
|
4668 |
] |
|
|
4669 |
} |
|
|
4670 |
], |
|
|
4671 |
"source": [ |
|
|
4672 |
"pdx.index.name = \"gene_id\"\n", |
|
|
4673 |
"ids = pdx.index\n", |
|
|
4674 |
"ids = list(set(ids[ids.duplicated()]))\n", |
|
|
4675 |
"print(\"Strings containing duplicated gene IDs:\",pdx.loc[ids,:].shape[0])\n", |
|
|
4676 |
"pdx = handle_dups(pdx,corr_thr = 0.75)\n" |
|
|
4677 |
] |
|
|
4678 |
}, |
|
|
4679 |
{ |
|
|
4680 |
"cell_type": "code", |
|
|
4681 |
"execution_count": 32, |
|
|
4682 |
"metadata": {}, |
|
|
4683 |
"outputs": [ |
|
|
4684 |
{ |
|
|
4685 |
"data": { |
|
|
4686 |
"text/plain": [ |
|
|
4687 |
"Text(0.5,0,'CN Averaged over all')" |
|
|
4688 |
] |
|
|
4689 |
}, |
|
|
4690 |
"execution_count": 32, |
|
|
4691 |
"metadata": {}, |
|
|
4692 |
"output_type": "execute_result" |
|
|
4693 |
}, |
|
|
4694 |
{ |
|
|
4695 |
"data": { |
|
|
4696 |
"image/png": 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SicBWwx5dGRERE1idUUOXS9pE0mbANcDJkk7otl1EREwMdbqGnmb7PuDvgdNtvxTYq9mwIiKiV+okgg0kzaB6yPx3Go4nIiJ6rE4i+Dfg+8BNtq+W9CyqewoiImIS6JoIbP+n7Rfbfnf5fLPtrqOGJJ0qabmk6zqWHSPpdkmLymvftQs/IiLWVpP3A3yFkW88+4zt2eV1UYPHj4iIGhpLBLavBO5uav8RETE++nGH8HskXVu6jjYdrZCkuZIWSFqwYsWKXsYXEdEqXW8ok/QkqjuJZ3WWt/1va3C8LwIfp3rm8ceB44H/MVJB2/OB+QCDg4Neg2NFREQNdeYaOh/4M7CQjieUrQnbdw69l3QyGY4aEdF3dRLBlrbHZbZRSTNsLysfD6R6HnJERPRRnUTwU0nb2V48lh1LOgPYHdhc0m1Uj7zcXdJsqq6hpcA7xxZuRESMtzqJYDfgMEm3UHUNCbDtF69uI9tzRlh8ythDjIiIJtVJBPs0HkVERPTNWKahjoiISShPGouIaLkkgoiIlksiiIhouSSCiIiWSyKIiGi5JIKIiJZLIoiIaLkkgoiIlksiiIhouSSCiIiWqzPXUKyhWUddWKvc0nmvbziSiIjRpUUQEdFySQQRES2XRBAR0XJJBBERLZdEEBHRchk1FLEW+jkyLKPSYrykRRAR0XKNJQJJp0paLum6jmWbSbpE0m/L302bOn5ERNTTZIvgK8Drhi07CrjU9nOBS8vniIjoo8YSge0rgbuHLd4fOK28Pw04oKnjR0REPb2+RjDd9rLy/o/A9B4fPyIihunbqCHbluTR1kuaC8wFmDlzZs/i6qbuSI1+7zMioq5etwjulDQDoPxdPlpB2/NtD9oeHBgY6FmAERFt0+tEcAFwaHl/KHB+j48fERHDNDl89AzgZ8DzJd0m6R3APGBvSb8F9iqfIyKijxq7RmB7ziirXt3UMSMiYuxyZ3FERMtlrqGIHhjLyLDMDRS9lhZBRETLJRFERLRcEkFERMslEUREtFwSQUREyyURRES0XBJBRETLJRFERLRcEkFERMslEUREtFymmIhYx4z3g4rq7q/u1Bbjvb/ov7QIIiJaLokgIqLlkggiIlouiSAiouWSCCIiWi6JICKi5ZIIIiJaLokgIqLl+nJDmaSlwP3Ao8BK24P9iCMiIvp7Z/Eetu/q4/EjIoJ0DUVEtF6/EoGBiyUtlDR3pAKS5kpaIGnBihUrehxeRER79CsR7GZ7R2Af4H9KeuXwArbn2x60PTgwMND7CCMiWqIvicD27eXvcuBcYOd+xBEREX1IBJKeKmnjoffAa4Dreh1HRERU+jFqaDpwrqSh43/D9vf6EEdERNCHRGD7ZmD7Xh83IiJGlieURUQjxvKktTzNrL9yH0FERMslEUREtFwSQUREyyURRES0XBJBRETLZdRQMZYRDhGT0WT6P1D3u2S0UiUtgoiIlksiiIhouSSCiIiWSyKIiGi5JIKIiJaT7X7H0NXg4KAXLFiwRttOppEQEdEfE3V0kaSFtge7lUuLICKi5ZIIIiJaLokgIqLlkggiIlouiSAiouUy11BExDhpYpRiL0YspUUQEdFySQQRES3Xl0Qg6XWSbpR0k6Sj+hFDRERUep4IJK0PfAHYB9gWmCNp217HERERlX60CHYGbrJ9s+1HgDOB/fsQR0RE0J9RQ1sAf+j4fBvw0uGFJM0F5paPD0i6sQexrY3Ngbv6HcQ6IPWwSupilQldFzpu3HY15npYy2M/s06hdXb4qO35wPx+x1GXpAV1Jnea7FIPq6QuVkldVNbVeuhH19DtwFYdn7csyyIiog/6kQiuBp4raWtJGwJvAS7oQxwREUEfuoZsr5T0HuD7wPrAqbaX9DqOBkyYbqyGpR5WSV2skrqorJP1MCEeTBMREc3JncURES2XRBAR0XJJBGMg6VRJyyVdN8r6p0n6tqRfSVoi6fBex9gLkraS9ENJ15fv+b4RykjSiWUakWsl7diPWJtWsy7eVupgsaSfStq+H7E2qU49dJR9iaSVkt7Yyxh7pW5dSNpd0qJS5opex/kEtvOq+QJeCewIXDfK+g8Dx5X3A8DdwIb9jruBepgB7Fjebwz8Bth2WJl9ge8CAnYBrup33H2si5cDm5b3+0zGuqhTD2Xd+sBlwEXAG/sddx//TUwDrgdmls9P72fMaRGMge0rqU7uoxYBNpYkYGopu7IXsfWS7WW2rynv7wduoLpjvNP+wOmu/ByYJmlGj0NtXJ26sP1T2/eUjz+nundmUqn5bwLgCOBbwPIehtdTNevircA5tn9fyvW1PpIIxtdJwAuAO4DFwPtsP9bfkJolaRawA3DVsFUjTSUy0olh0lhNXXR6B1VLadIarR4kbQEcCHyx91H1x2r+TTwP2FTS5ZIWSnp7r2PrtM5OMTFBvRZYBOwJPBu4RNKPbN/X37CaIWkq1a+790/W71hXnbqQtAdVItitl7H1Upd6+CxwpO3Hqkbz5NalLjYAdgJeDWwE/EzSz23/psdhPh5MjJ/DgXmuOv1uknQLsA3wi/6GNf4kTaH6R/512+eMUKQ1U4nUqAskvRj4ErCP7T/1Mr5eqVEPg8CZJQlsDuwraaXt83oYZk/UqIvbgD/ZfhB4UNKVwPZU1xN6Ll1D4+v3VBkeSdOB5wM39zWiBpRrIKcAN9g+YZRiFwBvL6OHdgH+bHtZz4LskTp1IWkmcA5wSL9+8TWtTj3Y3tr2LNuzgG8C756kSaDO/4/zgd0kbSDpKVQzMN/QqxiHS4tgDCSdAewObC7pNuBoYAqA7f8LfBz4iqTFVKNljrQ9YafeXY1dgUOAxZIWlWUfBmbC43VxEdXIoZuAv1C1liajOnXxMeDvgP9Tfg2v9Do4A+VaqlMPbdG1LmzfIOl7wLXAY8CXbI84LL0XMsVERETLpWsoIqLlkggiIlouiSAiouWSCCIiWi6JICKi5ZIIoqck/TdJZ0r6Xbm1/iJJz5M0S5IlHdFR9iRJh61mX4skndmTwNeSpMMkndTvOIaT9ED5O2u0WXVj8ksiiJ4pN9qcC1xu+9m2dwI+BEwvRZYD7yvPsu62rxdQzWT5CklPHaf4JsV9NZPle0TvJBFEL+0B/K3z5iLbv7L9o/JxBXApcGiNfc0BvgpcTDXTKZK2kfT4dB7lV+7i8n4nSVeUVsj3h2ZCLZN+fVbSAqoktJ+kqyT9UtIPyh3iSBqQdEmZO/5Lkm6VtHlZd7CkX5QWyv+TtH5Zfrik35SYdh3pS0jaTNJ5qp5X8HNJL5a0nqSlkqZ1lPutpOkljm9Jurq8di3rj5H0VUk/KfXSeYypki6VdI2qZyLsX6N+o0WSCKKXXgQs7FLmOOADQyfT1XgzcCZwBlVSwPavgQ0lbd1R5qwy78vnqea/3wk4Ffhkx742tD1o+3jgx8Autnco+//XUuZo4DLbL6SaHmEmPN4yeTOwq+3ZwKPA20qiOZYqAewGbDvK9zgW+KXtF1PdfXp6mbH2fKqZOpH0UuBW23cCnwM+Y/slwBuo5i8asi2wl+05w47xEHCg7R2pkvHxasOsb1FbmpCxTrF9s6SrqOZrH5GkQeAu27+XdDtwqqTNbN8NnE11Yp5X/r6Zas6nF1HNBgtVl1LnvEdndbzfkip5zAA2BG4py3ejnJhtf0/S0PMFXk01i+TVZd8bUXVxvZSqC2xFifksqqmHh9uN6oSO7csk/Z2kTUpMHwO+DLylI8a9gG07zuObqJrlEuAC238dqcqAT0l6JdV0BltQdcf9cYSy0UJJBNFLS4A6jyf8FNWv7tEe3zcH2EbS0vJ5E6qT6clUJ8z/lHQOYNu/lbQdsMT2y0bZ34Md7z8PnGD7Akm7A8d0iVXAabY/9ISF0gFdtuvmZ8BzJA0ABwCfKMvXo2qxPDTsePDE79HpbVRPzNvJ9t9KvT15LeOLSSRdQ9FLlwFPkjR3aEHpE39FZ6HSxXM9sN/wHUhaD3gTsF3HTJb7s6p76HdU3TMfZdWv6BuBAUkvK/uYIumFo8T4NFZNl915reIn5bhIeg2waVl+KfBGSU8v6zaT9EyqB5G8qvzCnwIcNMrxfkR1oqYknrts31emMj8XOIFqFsuhqasvpnrK11B9zB5lv8O/0/KSBPYAnlljm2iRJILomXJyOxDYqwwfXQL8OyN3UXySkR/p+Argdtt3dCy7kqq7ZOhRmGcBB1N1E2H7EaqWyHGSfkX18KCXjxLmMVQtioVA58yxxwKvKUMsDyox32/7euAjwMWSrgUuAWaUKbePofpl/xNGn2L4GGCnsu08nph8hr5HZ9fVe4HBcnH5euBdo+y309fLNouBtwO/rrFNtEhmH42oQdKTgEdtrywtiy+Wi8MRE16uEUTUMxM4u3RNPQL8Y5/jiRg3aRFERLRcrhFERLRcEkFERMslEUREtFwSQUREyyURRES03P8H9AxF0s+Zly8AAAAASUVORK5CYII=\n", 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4697 |
"text/plain": [ |
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4698 |
"<Figure size 432x288 with 1 Axes>" |
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4699 |
] |
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4700 |
}, |
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4701 |
"metadata": {}, |
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4702 |
"output_type": "display_data" |
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4703 |
} |
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4704 |
], |
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4705 |
"source": [ |
|
|
4706 |
"average_ploidies = pdx.apply(np.mean)\n", |
|
|
4707 |
"p = plt.hist(average_ploidies,bins=30)\n", |
|
|
4708 |
"plt.title(\"Ploidy in PDX samples\")\n", |
|
|
4709 |
"plt.ylabel(\"n samples\")\n", |
|
|
4710 |
"plt.xlabel(\"CN Averaged over all\")" |
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4711 |
] |
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|
4712 |
}, |
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4713 |
{ |
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4714 |
"cell_type": "code", |
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4715 |
"execution_count": 33, |
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4716 |
"metadata": {}, |
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4717 |
"outputs": [ |
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4718 |
{ |
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4719 |
"data": { |
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4720 |
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4721 |
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4734 |
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4737 |
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4738 |
" <th></th>\n", |
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4739 |
" <th>X-1004</th>\n", |
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4740 |
" <th>X-1008</th>\n", |
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4741 |
" <th>X-1027</th>\n", |
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4742 |
" <th>X-1095</th>\n", |
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4743 |
" <th>X-1119</th>\n", |
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4744 |
" <th>X-1156</th>\n", |
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4745 |
" <th>X-1167</th>\n", |
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4746 |
" <th>X-1169</th>\n", |
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4747 |
" <th>X-1172</th>\n", |
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|
4748 |
" <th>X-1173</th>\n", |
|
|
4749 |
" <th>...</th>\n", |
|
|
4750 |
" <th>X-5694</th>\n", |
|
|
4751 |
" <th>X-5696</th>\n", |
|
|
4752 |
" <th>X-5713</th>\n", |
|
|
4753 |
" <th>X-5717</th>\n", |
|
|
4754 |
" <th>X-5727</th>\n", |
|
|
4755 |
" <th>X-5739</th>\n", |
|
|
4756 |
" <th>X-5808</th>\n", |
|
|
4757 |
" <th>X-5959</th>\n", |
|
|
4758 |
" <th>X-5975</th>\n", |
|
|
4759 |
" <th>X-6047</th>\n", |
|
|
4760 |
" </tr>\n", |
|
|
4761 |
" <tr>\n", |
|
|
4762 |
" <th>gene_id</th>\n", |
|
|
4763 |
" <th></th>\n", |
|
|
4764 |
" <th></th>\n", |
|
|
4765 |
" <th></th>\n", |
|
|
4766 |
" <th></th>\n", |
|
|
4767 |
" <th></th>\n", |
|
|
4768 |
" <th></th>\n", |
|
|
4769 |
" <th></th>\n", |
|
|
4770 |
" <th></th>\n", |
|
|
4771 |
" <th></th>\n", |
|
|
4772 |
" <th></th>\n", |
|
|
4773 |
" <th></th>\n", |
|
|
4774 |
" <th></th>\n", |
|
|
4775 |
" <th></th>\n", |
|
|
4776 |
" <th></th>\n", |
|
|
4777 |
" <th></th>\n", |
|
|
4778 |
" <th></th>\n", |
|
|
4779 |
" <th></th>\n", |
|
|
4780 |
" <th></th>\n", |
|
|
4781 |
" <th></th>\n", |
|
|
4782 |
" <th></th>\n", |
|
|
4783 |
" <th></th>\n", |
|
|
4784 |
" </tr>\n", |
|
|
4785 |
" </thead>\n", |
|
|
4786 |
" <tbody>\n", |
|
|
4787 |
" <tr>\n", |
|
|
4788 |
" <th>A1BG</th>\n", |
|
|
4789 |
" <td>0.367371</td>\n", |
|
|
4790 |
" <td>-0.321928</td>\n", |
|
|
4791 |
" <td>0.117695</td>\n", |
|
|
4792 |
" <td>0.056584</td>\n", |
|
|
4793 |
" <td>0.000000</td>\n", |
|
|
4794 |
" <td>0.978196</td>\n", |
|
|
4795 |
" <td>0.028569</td>\n", |
|
|
4796 |
" <td>2.509696</td>\n", |
|
|
4797 |
" <td>0.117695</td>\n", |
|
|
4798 |
" <td>0.007196</td>\n", |
|
|
4799 |
" <td>...</td>\n", |
|
|
4800 |
" <td>0.056584</td>\n", |
|
|
4801 |
" <td>0.070389</td>\n", |
|
|
4802 |
" <td>0.097611</td>\n", |
|
|
4803 |
" <td>0.560715</td>\n", |
|
|
4804 |
" <td>0.042644</td>\n", |
|
|
4805 |
" <td>0.049631</td>\n", |
|
|
4806 |
" <td>-0.007232</td>\n", |
|
|
4807 |
" <td>0.049631</td>\n", |
|
|
4808 |
" <td>-0.483985</td>\n", |
|
|
4809 |
" <td>0.021480</td>\n", |
|
|
4810 |
" </tr>\n", |
|
|
4811 |
" <tr>\n", |
|
|
4812 |
" <th>A1BG-AS1</th>\n", |
|
|
4813 |
" <td>0.367371</td>\n", |
|
|
4814 |
" <td>-0.321928</td>\n", |
|
|
4815 |
" <td>0.117695</td>\n", |
|
|
4816 |
" <td>0.056584</td>\n", |
|
|
4817 |
" <td>0.000000</td>\n", |
|
|
4818 |
" <td>0.978196</td>\n", |
|
|
4819 |
" <td>0.028569</td>\n", |
|
|
4820 |
" <td>2.509696</td>\n", |
|
|
4821 |
" <td>0.117695</td>\n", |
|
|
4822 |
" <td>0.007196</td>\n", |
|
|
4823 |
" <td>...</td>\n", |
|
|
4824 |
" <td>0.056584</td>\n", |
|
|
4825 |
" <td>0.070389</td>\n", |
|
|
4826 |
" <td>0.097611</td>\n", |
|
|
4827 |
" <td>0.560715</td>\n", |
|
|
4828 |
" <td>0.042644</td>\n", |
|
|
4829 |
" <td>0.049631</td>\n", |
|
|
4830 |
" <td>-0.007232</td>\n", |
|
|
4831 |
" <td>0.049631</td>\n", |
|
|
4832 |
" <td>-0.483985</td>\n", |
|
|
4833 |
" <td>0.021480</td>\n", |
|
|
4834 |
" </tr>\n", |
|
|
4835 |
" <tr>\n", |
|
|
4836 |
" <th>A1CF</th>\n", |
|
|
4837 |
" <td>0.521051</td>\n", |
|
|
4838 |
" <td>0.570463</td>\n", |
|
|
4839 |
" <td>0.007196</td>\n", |
|
|
4840 |
" <td>0.042644</td>\n", |
|
|
4841 |
" <td>0.070389</td>\n", |
|
|
4842 |
" <td>-0.340075</td>\n", |
|
|
4843 |
" <td>0.007196</td>\n", |
|
|
4844 |
" <td>-0.286304</td>\n", |
|
|
4845 |
" <td>-0.081614</td>\n", |
|
|
4846 |
" <td>-0.007232</td>\n", |
|
|
4847 |
" <td>...</td>\n", |
|
|
4848 |
" <td>0.028569</td>\n", |
|
|
4849 |
" <td>-1.043943</td>\n", |
|
|
4850 |
" <td>-0.340075</td>\n", |
|
|
4851 |
" <td>0.056584</td>\n", |
|
|
4852 |
" <td>-0.036526</td>\n", |
|
|
4853 |
" <td>-0.058894</td>\n", |
|
|
4854 |
" <td>-0.377070</td>\n", |
|
|
4855 |
" <td>-0.643856</td>\n", |
|
|
4856 |
" <td>-0.588574</td>\n", |
|
|
4857 |
" <td>0.070389</td>\n", |
|
|
4858 |
" </tr>\n", |
|
|
4859 |
" </tbody>\n", |
|
|
4860 |
"</table>\n", |
|
|
4861 |
"<p>3 rows × 375 columns</p>\n", |
|
|
4862 |
"</div>" |
|
|
4863 |
], |
|
|
4864 |
"text/plain": [ |
|
|
4865 |
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 \\\n", |
|
|
4866 |
"gene_id \n", |
|
|
4867 |
"A1BG 0.367371 -0.321928 0.117695 0.056584 0.000000 0.978196 \n", |
|
|
4868 |
"A1BG-AS1 0.367371 -0.321928 0.117695 0.056584 0.000000 0.978196 \n", |
|
|
4869 |
"A1CF 0.521051 0.570463 0.007196 0.042644 0.070389 -0.340075 \n", |
|
|
4870 |
"\n", |
|
|
4871 |
" X-1167 X-1169 X-1172 X-1173 ... X-5694 \\\n", |
|
|
4872 |
"gene_id ... \n", |
|
|
4873 |
"A1BG 0.028569 2.509696 0.117695 0.007196 ... 0.056584 \n", |
|
|
4874 |
"A1BG-AS1 0.028569 2.509696 0.117695 0.007196 ... 0.056584 \n", |
|
|
4875 |
"A1CF 0.007196 -0.286304 -0.081614 -0.007232 ... 0.028569 \n", |
|
|
4876 |
"\n", |
|
|
4877 |
" X-5696 X-5713 X-5717 X-5727 X-5739 X-5808 \\\n", |
|
|
4878 |
"gene_id \n", |
|
|
4879 |
"A1BG 0.070389 0.097611 0.560715 0.042644 0.049631 -0.007232 \n", |
|
|
4880 |
"A1BG-AS1 0.070389 0.097611 0.560715 0.042644 0.049631 -0.007232 \n", |
|
|
4881 |
"A1CF -1.043943 -0.340075 0.056584 -0.036526 -0.058894 -0.377070 \n", |
|
|
4882 |
"\n", |
|
|
4883 |
" X-5959 X-5975 X-6047 \n", |
|
|
4884 |
"gene_id \n", |
|
|
4885 |
"A1BG 0.049631 -0.483985 0.021480 \n", |
|
|
4886 |
"A1BG-AS1 0.049631 -0.483985 0.021480 \n", |
|
|
4887 |
"A1CF -0.643856 -0.588574 0.070389 \n", |
|
|
4888 |
"\n", |
|
|
4889 |
"[3 rows x 375 columns]" |
|
|
4890 |
] |
|
|
4891 |
}, |
|
|
4892 |
"execution_count": 33, |
|
|
4893 |
"metadata": {}, |
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|
4894 |
"output_type": "execute_result" |
|
|
4895 |
} |
|
|
4896 |
], |
|
|
4897 |
"source": [ |
|
|
4898 |
"pdx = pdx.applymap(lambda x: np.log2(x/2))\n", |
|
|
4899 |
"pdx.head(3)" |
|
|
4900 |
] |
|
|
4901 |
}, |
|
|
4902 |
{ |
|
|
4903 |
"cell_type": "code", |
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|
4904 |
"execution_count": 34, |
|
|
4905 |
"metadata": {}, |
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|
4906 |
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|
4907 |
{ |
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4908 |
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|
4926 |
" <tr style=\"text-align: right;\">\n", |
|
|
4927 |
" <th></th>\n", |
|
|
4928 |
" <th>X-1004</th>\n", |
|
|
4929 |
" <th>X-1008</th>\n", |
|
|
4930 |
" <th>X-1027</th>\n", |
|
|
4931 |
" <th>X-1095</th>\n", |
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4932 |
" <th>X-1119</th>\n", |
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4933 |
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4934 |
" <th>X-1167</th>\n", |
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4935 |
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4936 |
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4937 |
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4938 |
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|
|
4939 |
" <th>X-5694</th>\n", |
|
|
4940 |
" <th>X-5696</th>\n", |
|
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4941 |
" <th>X-5713</th>\n", |
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4942 |
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4943 |
" <th>X-5727</th>\n", |
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4944 |
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4945 |
" <th>X-5808</th>\n", |
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|
4946 |
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4947 |
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|
4948 |
" <th>X-6047</th>\n", |
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4949 |
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|
4950 |
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|
|
4951 |
" <th>gene_id</th>\n", |
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|
4952 |
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4953 |
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4954 |
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4955 |
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4956 |
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4957 |
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4958 |
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4959 |
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4960 |
" <th></th>\n", |
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4961 |
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4962 |
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4963 |
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4964 |
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4965 |
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4966 |
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4967 |
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4968 |
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4969 |
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4970 |
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4971 |
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|
|
4972 |
" <th></th>\n", |
|
|
4973 |
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|
|
4974 |
" </thead>\n", |
|
|
4975 |
" <tbody>\n", |
|
|
4976 |
" <tr>\n", |
|
|
4977 |
" <th>A1BG</th>\n", |
|
|
4978 |
" <td>0.367371</td>\n", |
|
|
4979 |
" <td>-0.321928</td>\n", |
|
|
4980 |
" <td>0.0</td>\n", |
|
|
4981 |
" <td>0.0</td>\n", |
|
|
4982 |
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|
|
4983 |
" <td>0.978196</td>\n", |
|
|
4984 |
" <td>0.0</td>\n", |
|
|
4985 |
" <td>2.509696</td>\n", |
|
|
4986 |
" <td>0.0</td>\n", |
|
|
4987 |
" <td>0.0</td>\n", |
|
|
4988 |
" <td>...</td>\n", |
|
|
4989 |
" <td>0.0</td>\n", |
|
|
4990 |
" <td>0.000000</td>\n", |
|
|
4991 |
" <td>0.000000</td>\n", |
|
|
4992 |
" <td>0.560715</td>\n", |
|
|
4993 |
" <td>0.0</td>\n", |
|
|
4994 |
" <td>0.0</td>\n", |
|
|
4995 |
" <td>0.00000</td>\n", |
|
|
4996 |
" <td>0.000000</td>\n", |
|
|
4997 |
" <td>-0.483985</td>\n", |
|
|
4998 |
" <td>0.0</td>\n", |
|
|
4999 |
" </tr>\n", |
|
|
5000 |
" <tr>\n", |
|
|
5001 |
" <th>A1BG-AS1</th>\n", |
|
|
5002 |
" <td>0.367371</td>\n", |
|
|
5003 |
" <td>-0.321928</td>\n", |
|
|
5004 |
" <td>0.0</td>\n", |
|
|
5005 |
" <td>0.0</td>\n", |
|
|
5006 |
" <td>0.0</td>\n", |
|
|
5007 |
" <td>0.978196</td>\n", |
|
|
5008 |
" <td>0.0</td>\n", |
|
|
5009 |
" <td>2.509696</td>\n", |
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|
5010 |
" <td>0.0</td>\n", |
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|
5011 |
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|
5012 |
" <td>...</td>\n", |
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|
5013 |
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|
|
5014 |
" <td>0.000000</td>\n", |
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|
5015 |
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|
5016 |
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|
5017 |
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|
5018 |
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|
5019 |
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|
|
5020 |
" <td>0.000000</td>\n", |
|
|
5021 |
" <td>-0.483985</td>\n", |
|
|
5022 |
" <td>0.0</td>\n", |
|
|
5023 |
" </tr>\n", |
|
|
5024 |
" <tr>\n", |
|
|
5025 |
" <th>A1CF</th>\n", |
|
|
5026 |
" <td>0.521051</td>\n", |
|
|
5027 |
" <td>0.570463</td>\n", |
|
|
5028 |
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|
5029 |
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|
5030 |
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|
5031 |
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|
5032 |
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|
|
5033 |
" <td>-0.286304</td>\n", |
|
|
5034 |
" <td>0.0</td>\n", |
|
|
5035 |
" <td>0.0</td>\n", |
|
|
5036 |
" <td>...</td>\n", |
|
|
5037 |
" <td>0.0</td>\n", |
|
|
5038 |
" <td>-1.043943</td>\n", |
|
|
5039 |
" <td>-0.340075</td>\n", |
|
|
5040 |
" <td>0.000000</td>\n", |
|
|
5041 |
" <td>0.0</td>\n", |
|
|
5042 |
" <td>0.0</td>\n", |
|
|
5043 |
" <td>-0.37707</td>\n", |
|
|
5044 |
" <td>-0.643856</td>\n", |
|
|
5045 |
" <td>-0.588574</td>\n", |
|
|
5046 |
" <td>0.0</td>\n", |
|
|
5047 |
" </tr>\n", |
|
|
5048 |
" </tbody>\n", |
|
|
5049 |
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|
5050 |
"<p>3 rows × 375 columns</p>\n", |
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|
5051 |
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5052 |
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5053 |
"text/plain": [ |
|
|
5054 |
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 \\\n", |
|
|
5055 |
"gene_id \n", |
|
|
5056 |
"A1BG 0.367371 -0.321928 0.0 0.0 0.0 0.978196 0.0 \n", |
|
|
5057 |
"A1BG-AS1 0.367371 -0.321928 0.0 0.0 0.0 0.978196 0.0 \n", |
|
|
5058 |
"A1CF 0.521051 0.570463 0.0 0.0 0.0 -0.340075 0.0 \n", |
|
|
5059 |
"\n", |
|
|
5060 |
" X-1169 X-1172 X-1173 ... X-5694 X-5696 X-5713 \\\n", |
|
|
5061 |
"gene_id ... \n", |
|
|
5062 |
"A1BG 2.509696 0.0 0.0 ... 0.0 0.000000 0.000000 \n", |
|
|
5063 |
"A1BG-AS1 2.509696 0.0 0.0 ... 0.0 0.000000 0.000000 \n", |
|
|
5064 |
"A1CF -0.286304 0.0 0.0 ... 0.0 -1.043943 -0.340075 \n", |
|
|
5065 |
"\n", |
|
|
5066 |
" X-5717 X-5727 X-5739 X-5808 X-5959 X-5975 X-6047 \n", |
|
|
5067 |
"gene_id \n", |
|
|
5068 |
"A1BG 0.560715 0.0 0.0 0.00000 0.000000 -0.483985 0.0 \n", |
|
|
5069 |
"A1BG-AS1 0.560715 0.0 0.0 0.00000 0.000000 -0.483985 0.0 \n", |
|
|
5070 |
"A1CF 0.000000 0.0 0.0 -0.37707 -0.643856 -0.588574 0.0 \n", |
|
|
5071 |
"\n", |
|
|
5072 |
"[3 rows x 375 columns]" |
|
|
5073 |
] |
|
|
5074 |
}, |
|
|
5075 |
"execution_count": 34, |
|
|
5076 |
"metadata": {}, |
|
|
5077 |
"output_type": "execute_result" |
|
|
5078 |
} |
|
|
5079 |
], |
|
|
5080 |
"source": [ |
|
|
5081 |
"pdx = pdx.applymap(lambda x : clean_logR(x, pos_seg_mean_thr, neg_seg_mean_thr))\n", |
|
|
5082 |
"pdx.head(3)" |
|
|
5083 |
] |
|
|
5084 |
}, |
|
|
5085 |
{ |
|
|
5086 |
"cell_type": "code", |
|
|
5087 |
"execution_count": 35, |
|
|
5088 |
"metadata": {}, |
|
|
5089 |
"outputs": [ |
|
|
5090 |
{ |
|
|
5091 |
"name": "stdout", |
|
|
5092 |
"output_type": "stream", |
|
|
5093 |
"text": [ |
|
|
5094 |
"Mapped: 23313 \n", |
|
|
5095 |
"\tdirectly via main_mapper 21188 \n", |
|
|
5096 |
"\tvia alternative mapper 466 \n", |
|
|
5097 |
"\tvia one of multiple synonyms in alternative mapper 926 \n", |
|
|
5098 |
"\tLOC 733 \n", |
|
|
5099 |
"Unmapped: 200 \n", |
|
|
5100 |
"\trecognized symbols without Entrez ID 0 \n", |
|
|
5101 |
"\tmultiple query_ids map to the same target_id 0 \n", |
|
|
5102 |
"\tquery_ids map to multiple target_ids in the main mapper 0 \n", |
|
|
5103 |
"\tquery_ids map to multiple target_ids in the alternative mapper 52 \n", |
|
|
5104 |
"\tLOC not found in Entrez 29 \n", |
|
|
5105 |
"\tNot found at all: 119\n", |
|
|
5106 |
"Warning: query IDs mapping to duplicated target IDs in mapping table: 77\n", |
|
|
5107 |
"Warning: query IDs not mapped to any target IDs excluded: 200\n" |
|
|
5108 |
] |
|
|
5109 |
}, |
|
|
5110 |
{ |
|
|
5111 |
"name": "stderr", |
|
|
5112 |
"output_type": "stream", |
|
|
5113 |
"text": [ |
|
|
5114 |
"IDs mapped to multiple target IDs are kept:\n", |
|
|
5115 |
" [143872, 286464, 51463, 642826, 653067, 399761, 647060, 284565, 84631, 161176, 341019, 83869, 9502, 83871, 728113, 729438, 4253, 645425, 26165, 6218, 728695, 100132948, 100134869, 84316, 200030, 642658, 100302179, 401508, 119016, 84458, 574445, 26095, 84968, 80759, 3192, 387707, 79741]\n" |
|
|
5116 |
] |
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5117 |
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5118 |
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5119 |
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5124 |
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5125 |
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5134 |
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5135 |
"<table border=\"1\" class=\"dataframe\">\n", |
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|
5136 |
" <thead>\n", |
|
|
5137 |
" <tr style=\"text-align: right;\">\n", |
|
|
5138 |
" <th></th>\n", |
|
|
5139 |
" <th>X-1004</th>\n", |
|
|
5140 |
" <th>X-1008</th>\n", |
|
|
5141 |
" <th>X-1027</th>\n", |
|
|
5142 |
" <th>X-1095</th>\n", |
|
|
5143 |
" <th>X-1119</th>\n", |
|
|
5144 |
" <th>X-1156</th>\n", |
|
|
5145 |
" <th>X-1167</th>\n", |
|
|
5146 |
" <th>X-1169</th>\n", |
|
|
5147 |
" <th>X-1172</th>\n", |
|
|
5148 |
" <th>X-1173</th>\n", |
|
|
5149 |
" <th>...</th>\n", |
|
|
5150 |
" <th>X-5694</th>\n", |
|
|
5151 |
" <th>X-5696</th>\n", |
|
|
5152 |
" <th>X-5713</th>\n", |
|
|
5153 |
" <th>X-5717</th>\n", |
|
|
5154 |
" <th>X-5727</th>\n", |
|
|
5155 |
" <th>X-5739</th>\n", |
|
|
5156 |
" <th>X-5808</th>\n", |
|
|
5157 |
" <th>X-5959</th>\n", |
|
|
5158 |
" <th>X-5975</th>\n", |
|
|
5159 |
" <th>X-6047</th>\n", |
|
|
5160 |
" </tr>\n", |
|
|
5161 |
" <tr>\n", |
|
|
5162 |
" <th>gene_id</th>\n", |
|
|
5163 |
" <th></th>\n", |
|
|
5164 |
" <th></th>\n", |
|
|
5165 |
" <th></th>\n", |
|
|
5166 |
" <th></th>\n", |
|
|
5167 |
" <th></th>\n", |
|
|
5168 |
" <th></th>\n", |
|
|
5169 |
" <th></th>\n", |
|
|
5170 |
" <th></th>\n", |
|
|
5171 |
" <th></th>\n", |
|
|
5172 |
" <th></th>\n", |
|
|
5173 |
" <th></th>\n", |
|
|
5174 |
" <th></th>\n", |
|
|
5175 |
" <th></th>\n", |
|
|
5176 |
" <th></th>\n", |
|
|
5177 |
" <th></th>\n", |
|
|
5178 |
" <th></th>\n", |
|
|
5179 |
" <th></th>\n", |
|
|
5180 |
" <th></th>\n", |
|
|
5181 |
" <th></th>\n", |
|
|
5182 |
" <th></th>\n", |
|
|
5183 |
" <th></th>\n", |
|
|
5184 |
" </tr>\n", |
|
|
5185 |
" </thead>\n", |
|
|
5186 |
" <tbody>\n", |
|
|
5187 |
" <tr>\n", |
|
|
5188 |
" <th>1</th>\n", |
|
|
5189 |
" <td>0.367371</td>\n", |
|
|
5190 |
" <td>-0.321928</td>\n", |
|
|
5191 |
" <td>0.0</td>\n", |
|
|
5192 |
" <td>0.000000</td>\n", |
|
|
5193 |
" <td>0.0</td>\n", |
|
|
5194 |
" <td>0.978196</td>\n", |
|
|
5195 |
" <td>0.0</td>\n", |
|
|
5196 |
" <td>2.509696</td>\n", |
|
|
5197 |
" <td>0.000000</td>\n", |
|
|
5198 |
" <td>0.0</td>\n", |
|
|
5199 |
" <td>...</td>\n", |
|
|
5200 |
" <td>0.0</td>\n", |
|
|
5201 |
" <td>0.0</td>\n", |
|
|
5202 |
" <td>0.0</td>\n", |
|
|
5203 |
" <td>0.560715</td>\n", |
|
|
5204 |
" <td>0.0</td>\n", |
|
|
5205 |
" <td>0.000000</td>\n", |
|
|
5206 |
" <td>0.000000</td>\n", |
|
|
5207 |
" <td>0.000000</td>\n", |
|
|
5208 |
" <td>-0.483985</td>\n", |
|
|
5209 |
" <td>0.0</td>\n", |
|
|
5210 |
" </tr>\n", |
|
|
5211 |
" <tr>\n", |
|
|
5212 |
" <th>2</th>\n", |
|
|
5213 |
" <td>0.761285</td>\n", |
|
|
5214 |
" <td>0.000000</td>\n", |
|
|
5215 |
" <td>0.0</td>\n", |
|
|
5216 |
" <td>0.500802</td>\n", |
|
|
5217 |
" <td>0.0</td>\n", |
|
|
5218 |
" <td>0.700440</td>\n", |
|
|
5219 |
" <td>0.0</td>\n", |
|
|
5220 |
" <td>0.000000</td>\n", |
|
|
5221 |
" <td>0.201634</td>\n", |
|
|
5222 |
" <td>0.0</td>\n", |
|
|
5223 |
" <td>...</td>\n", |
|
|
5224 |
" <td>0.0</td>\n", |
|
|
5225 |
" <td>0.0</td>\n", |
|
|
5226 |
" <td>0.0</td>\n", |
|
|
5227 |
" <td>0.739848</td>\n", |
|
|
5228 |
" <td>0.0</td>\n", |
|
|
5229 |
" <td>0.739848</td>\n", |
|
|
5230 |
" <td>0.327687</td>\n", |
|
|
5231 |
" <td>-0.494109</td>\n", |
|
|
5232 |
" <td>-0.535332</td>\n", |
|
|
5233 |
" <td>0.0</td>\n", |
|
|
5234 |
" </tr>\n", |
|
|
5235 |
" <tr>\n", |
|
|
5236 |
" <th>3</th>\n", |
|
|
5237 |
" <td>0.761285</td>\n", |
|
|
5238 |
" <td>0.000000</td>\n", |
|
|
5239 |
" <td>0.0</td>\n", |
|
|
5240 |
" <td>0.500802</td>\n", |
|
|
5241 |
" <td>0.0</td>\n", |
|
|
5242 |
" <td>0.700440</td>\n", |
|
|
5243 |
" <td>0.0</td>\n", |
|
|
5244 |
" <td>0.000000</td>\n", |
|
|
5245 |
" <td>0.201634</td>\n", |
|
|
5246 |
" <td>0.0</td>\n", |
|
|
5247 |
" <td>...</td>\n", |
|
|
5248 |
" <td>0.0</td>\n", |
|
|
5249 |
" <td>0.0</td>\n", |
|
|
5250 |
" <td>0.0</td>\n", |
|
|
5251 |
" <td>0.739848</td>\n", |
|
|
5252 |
" <td>0.0</td>\n", |
|
|
5253 |
" <td>0.739848</td>\n", |
|
|
5254 |
" <td>0.327687</td>\n", |
|
|
5255 |
" <td>-0.494109</td>\n", |
|
|
5256 |
" <td>-0.535332</td>\n", |
|
|
5257 |
" <td>0.0</td>\n", |
|
|
5258 |
" </tr>\n", |
|
|
5259 |
" </tbody>\n", |
|
|
5260 |
"</table>\n", |
|
|
5261 |
"<p>3 rows × 375 columns</p>\n", |
|
|
5262 |
"</div>" |
|
|
5263 |
], |
|
|
5264 |
"text/plain": [ |
|
|
5265 |
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 \\\n", |
|
|
5266 |
"gene_id \n", |
|
|
5267 |
"1 0.367371 -0.321928 0.0 0.000000 0.0 0.978196 0.0 \n", |
|
|
5268 |
"2 0.761285 0.000000 0.0 0.500802 0.0 0.700440 0.0 \n", |
|
|
5269 |
"3 0.761285 0.000000 0.0 0.500802 0.0 0.700440 0.0 \n", |
|
|
5270 |
"\n", |
|
|
5271 |
" X-1169 X-1172 X-1173 ... X-5694 X-5696 X-5713 X-5717 \\\n", |
|
|
5272 |
"gene_id ... \n", |
|
|
5273 |
"1 2.509696 0.000000 0.0 ... 0.0 0.0 0.0 0.560715 \n", |
|
|
5274 |
"2 0.000000 0.201634 0.0 ... 0.0 0.0 0.0 0.739848 \n", |
|
|
5275 |
"3 0.000000 0.201634 0.0 ... 0.0 0.0 0.0 0.739848 \n", |
|
|
5276 |
"\n", |
|
|
5277 |
" X-5727 X-5739 X-5808 X-5959 X-5975 X-6047 \n", |
|
|
5278 |
"gene_id \n", |
|
|
5279 |
"1 0.0 0.000000 0.000000 0.000000 -0.483985 0.0 \n", |
|
|
5280 |
"2 0.0 0.739848 0.327687 -0.494109 -0.535332 0.0 \n", |
|
|
5281 |
"3 0.0 0.739848 0.327687 -0.494109 -0.535332 0.0 \n", |
|
|
5282 |
"\n", |
|
|
5283 |
"[3 rows x 375 columns]" |
|
|
5284 |
] |
|
|
5285 |
}, |
|
|
5286 |
"execution_count": 35, |
|
|
5287 |
"metadata": {}, |
|
|
5288 |
"output_type": "execute_result" |
|
|
5289 |
} |
|
|
5290 |
], |
|
|
5291 |
"source": [ |
|
|
5292 |
"pdx,query2target,not_mapped = apply_mappers(pdx, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"keep\")\n", |
|
|
5293 |
"pdx.head(3)" |
|
|
5294 |
] |
|
|
5295 |
}, |
|
|
5296 |
{ |
|
|
5297 |
"cell_type": "code", |
|
|
5298 |
"execution_count": 36, |
|
|
5299 |
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|
|
5300 |
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5301 |
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5302 |
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5310 |
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5313 |
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5317 |
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5319 |
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|
5320 |
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|
|
5321 |
" <th></th>\n", |
|
|
5322 |
" <th>X-1004</th>\n", |
|
|
5323 |
" <th>X-1008</th>\n", |
|
|
5324 |
" <th>X-1027</th>\n", |
|
|
5325 |
" <th>X-1095</th>\n", |
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|
5326 |
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|
5327 |
" <th>X-1156</th>\n", |
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|
5328 |
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|
|
5329 |
" <th>X-1169</th>\n", |
|
|
5330 |
" <th>X-1172</th>\n", |
|
|
5331 |
" <th>X-1173</th>\n", |
|
|
5332 |
" <th>...</th>\n", |
|
|
5333 |
" <th>X-5694</th>\n", |
|
|
5334 |
" <th>X-5696</th>\n", |
|
|
5335 |
" <th>X-5713</th>\n", |
|
|
5336 |
" <th>X-5717</th>\n", |
|
|
5337 |
" <th>X-5727</th>\n", |
|
|
5338 |
" <th>X-5739</th>\n", |
|
|
5339 |
" <th>X-5808</th>\n", |
|
|
5340 |
" <th>X-5959</th>\n", |
|
|
5341 |
" <th>X-5975</th>\n", |
|
|
5342 |
" <th>X-6047</th>\n", |
|
|
5343 |
" </tr>\n", |
|
|
5344 |
" <tr>\n", |
|
|
5345 |
" <th>gene_id</th>\n", |
|
|
5346 |
" <th></th>\n", |
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|
5347 |
" <th></th>\n", |
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|
5348 |
" <th></th>\n", |
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|
5349 |
" <th></th>\n", |
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5350 |
" <th></th>\n", |
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5351 |
" <th></th>\n", |
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5352 |
" <th></th>\n", |
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|
5353 |
" <th></th>\n", |
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5354 |
" <th></th>\n", |
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5355 |
" <th></th>\n", |
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5356 |
" <th></th>\n", |
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5357 |
" <th></th>\n", |
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5358 |
" <th></th>\n", |
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5359 |
" <th></th>\n", |
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5360 |
" <th></th>\n", |
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5361 |
" <th></th>\n", |
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5362 |
" <th></th>\n", |
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5363 |
" <th></th>\n", |
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|
5364 |
" <th></th>\n", |
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5365 |
" <th></th>\n", |
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|
5366 |
" <th></th>\n", |
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|
5367 |
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5368 |
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|
|
5369 |
" <tbody>\n", |
|
|
5370 |
" <tr>\n", |
|
|
5371 |
" <th>143872</th>\n", |
|
|
5372 |
" <td>0.000000</td>\n", |
|
|
5373 |
" <td>0.560715</td>\n", |
|
|
5374 |
" <td>0.000000</td>\n", |
|
|
5375 |
" <td>0.000000</td>\n", |
|
|
5376 |
" <td>0.000000</td>\n", |
|
|
5377 |
" <td>-0.330973</td>\n", |
|
|
5378 |
" <td>0.000000</td>\n", |
|
|
5379 |
" <td>-0.367732</td>\n", |
|
|
5380 |
" <td>0.350497</td>\n", |
|
|
5381 |
" <td>0.000000</td>\n", |
|
|
5382 |
" <td>...</td>\n", |
|
|
5383 |
" <td>0.000000</td>\n", |
|
|
5384 |
" <td>-0.349235</td>\n", |
|
|
5385 |
" <td>0.000000</td>\n", |
|
|
5386 |
" <td>-0.321928</td>\n", |
|
|
5387 |
" <td>-1.014500</td>\n", |
|
|
5388 |
" <td>-0.588574</td>\n", |
|
|
5389 |
" <td>0.000000</td>\n", |
|
|
5390 |
" <td>0.000000</td>\n", |
|
|
5391 |
" <td>0.000000</td>\n", |
|
|
5392 |
" <td>-0.514573</td>\n", |
|
|
5393 |
" </tr>\n", |
|
|
5394 |
" <tr>\n", |
|
|
5395 |
" <th>143872</th>\n", |
|
|
5396 |
" <td>0.000000</td>\n", |
|
|
5397 |
" <td>0.560715</td>\n", |
|
|
5398 |
" <td>0.000000</td>\n", |
|
|
5399 |
" <td>0.000000</td>\n", |
|
|
5400 |
" <td>0.000000</td>\n", |
|
|
5401 |
" <td>-0.330973</td>\n", |
|
|
5402 |
" <td>0.000000</td>\n", |
|
|
5403 |
" <td>-0.367732</td>\n", |
|
|
5404 |
" <td>0.350497</td>\n", |
|
|
5405 |
" <td>0.000000</td>\n", |
|
|
5406 |
" <td>...</td>\n", |
|
|
5407 |
" <td>0.000000</td>\n", |
|
|
5408 |
" <td>-0.349235</td>\n", |
|
|
5409 |
" <td>0.000000</td>\n", |
|
|
5410 |
" <td>-0.321928</td>\n", |
|
|
5411 |
" <td>-1.014500</td>\n", |
|
|
5412 |
" <td>-0.588574</td>\n", |
|
|
5413 |
" <td>0.000000</td>\n", |
|
|
5414 |
" <td>0.000000</td>\n", |
|
|
5415 |
" <td>0.000000</td>\n", |
|
|
5416 |
" <td>-0.514573</td>\n", |
|
|
5417 |
" </tr>\n", |
|
|
5418 |
" <tr>\n", |
|
|
5419 |
" <th>286464</th>\n", |
|
|
5420 |
" <td>0.000000</td>\n", |
|
|
5421 |
" <td>0.378512</td>\n", |
|
|
5422 |
" <td>0.000000</td>\n", |
|
|
5423 |
" <td>0.550901</td>\n", |
|
|
5424 |
" <td>0.000000</td>\n", |
|
|
5425 |
" <td>-0.524915</td>\n", |
|
|
5426 |
" <td>0.000000</td>\n", |
|
|
5427 |
" <td>-0.902389</td>\n", |
|
|
5428 |
" <td>-1.321928</td>\n", |
|
|
5429 |
" <td>0.367371</td>\n", |
|
|
5430 |
" <td>...</td>\n", |
|
|
5431 |
" <td>0.000000</td>\n", |
|
|
5432 |
" <td>-1.014500</td>\n", |
|
|
5433 |
" <td>0.718088</td>\n", |
|
|
5434 |
" <td>0.000000</td>\n", |
|
|
5435 |
" <td>-1.014500</td>\n", |
|
|
5436 |
" <td>0.000000</td>\n", |
|
|
5437 |
" <td>0.000000</td>\n", |
|
|
5438 |
" <td>0.000000</td>\n", |
|
|
5439 |
" <td>-1.494109</td>\n", |
|
|
5440 |
" <td>-1.494109</td>\n", |
|
|
5441 |
" </tr>\n", |
|
|
5442 |
" <tr>\n", |
|
|
5443 |
" <th>286464</th>\n", |
|
|
5444 |
" <td>0.000000</td>\n", |
|
|
5445 |
" <td>0.378512</td>\n", |
|
|
5446 |
" <td>0.000000</td>\n", |
|
|
5447 |
" <td>0.550901</td>\n", |
|
|
5448 |
" <td>0.000000</td>\n", |
|
|
5449 |
" <td>-0.524915</td>\n", |
|
|
5450 |
" <td>0.000000</td>\n", |
|
|
5451 |
" <td>-0.902389</td>\n", |
|
|
5452 |
" <td>-1.321928</td>\n", |
|
|
5453 |
" <td>0.367371</td>\n", |
|
|
5454 |
" <td>...</td>\n", |
|
|
5455 |
" <td>0.000000</td>\n", |
|
|
5456 |
" <td>-1.014500</td>\n", |
|
|
5457 |
" <td>0.718088</td>\n", |
|
|
5458 |
" <td>0.000000</td>\n", |
|
|
5459 |
" <td>-1.014500</td>\n", |
|
|
5460 |
" <td>0.000000</td>\n", |
|
|
5461 |
" <td>0.000000</td>\n", |
|
|
5462 |
" <td>0.000000</td>\n", |
|
|
5463 |
" <td>-1.494109</td>\n", |
|
|
5464 |
" <td>-1.494109</td>\n", |
|
|
5465 |
" </tr>\n", |
|
|
5466 |
" <tr>\n", |
|
|
5467 |
" <th>286464</th>\n", |
|
|
5468 |
" <td>0.000000</td>\n", |
|
|
5469 |
" <td>0.378512</td>\n", |
|
|
5470 |
" <td>0.000000</td>\n", |
|
|
5471 |
" <td>0.550901</td>\n", |
|
|
5472 |
" <td>0.000000</td>\n", |
|
|
5473 |
" <td>-0.524915</td>\n", |
|
|
5474 |
" <td>0.000000</td>\n", |
|
|
5475 |
" <td>-0.902389</td>\n", |
|
|
5476 |
" <td>-1.321928</td>\n", |
|
|
5477 |
" <td>0.367371</td>\n", |
|
|
5478 |
" <td>...</td>\n", |
|
|
5479 |
" <td>0.000000</td>\n", |
|
|
5480 |
" <td>-1.014500</td>\n", |
|
|
5481 |
" <td>0.718088</td>\n", |
|
|
5482 |
" <td>0.000000</td>\n", |
|
|
5483 |
" <td>-1.014500</td>\n", |
|
|
5484 |
" <td>0.000000</td>\n", |
|
|
5485 |
" <td>0.000000</td>\n", |
|
|
5486 |
" <td>0.000000</td>\n", |
|
|
5487 |
" <td>-1.494109</td>\n", |
|
|
5488 |
" <td>-1.494109</td>\n", |
|
|
5489 |
" </tr>\n", |
|
|
5490 |
" <tr>\n", |
|
|
5491 |
" <th>51463</th>\n", |
|
|
5492 |
" <td>1.238787</td>\n", |
|
|
5493 |
" <td>1.090853</td>\n", |
|
|
5494 |
" <td>0.000000</td>\n", |
|
|
5495 |
" <td>0.000000</td>\n", |
|
|
5496 |
" <td>0.000000</td>\n", |
|
|
5497 |
" <td>1.839960</td>\n", |
|
|
5498 |
" <td>0.000000</td>\n", |
|
|
5499 |
" <td>0.448901</td>\n", |
|
|
5500 |
" <td>0.000000</td>\n", |
|
|
5501 |
" <td>0.000000</td>\n", |
|
|
5502 |
" <td>...</td>\n", |
|
|
5503 |
" <td>0.469886</td>\n", |
|
|
5504 |
" <td>0.000000</td>\n", |
|
|
5505 |
" <td>0.618239</td>\n", |
|
|
5506 |
" <td>0.201634</td>\n", |
|
|
5507 |
" <td>0.000000</td>\n", |
|
|
5508 |
" <td>-0.260152</td>\n", |
|
|
5509 |
" <td>-0.349235</td>\n", |
|
|
5510 |
" <td>0.000000</td>\n", |
|
|
5511 |
" <td>0.469886</td>\n", |
|
|
5512 |
" <td>0.000000</td>\n", |
|
|
5513 |
" </tr>\n", |
|
|
5514 |
" <tr>\n", |
|
|
5515 |
" <th>51463</th>\n", |
|
|
5516 |
" <td>1.238787</td>\n", |
|
|
5517 |
" <td>1.090853</td>\n", |
|
|
5518 |
" <td>0.000000</td>\n", |
|
|
5519 |
" <td>0.000000</td>\n", |
|
|
5520 |
" <td>0.000000</td>\n", |
|
|
5521 |
" <td>1.839960</td>\n", |
|
|
5522 |
" <td>0.000000</td>\n", |
|
|
5523 |
" <td>0.448901</td>\n", |
|
|
5524 |
" <td>0.000000</td>\n", |
|
|
5525 |
" <td>0.000000</td>\n", |
|
|
5526 |
" <td>...</td>\n", |
|
|
5527 |
" <td>0.438293</td>\n", |
|
|
5528 |
" <td>0.000000</td>\n", |
|
|
5529 |
" <td>0.618239</td>\n", |
|
|
5530 |
" <td>0.201634</td>\n", |
|
|
5531 |
" <td>0.000000</td>\n", |
|
|
5532 |
" <td>-0.260152</td>\n", |
|
|
5533 |
" <td>0.000000</td>\n", |
|
|
5534 |
" <td>0.000000</td>\n", |
|
|
5535 |
" <td>0.469886</td>\n", |
|
|
5536 |
" <td>0.000000</td>\n", |
|
|
5537 |
" </tr>\n", |
|
|
5538 |
" <tr>\n", |
|
|
5539 |
" <th>642826</th>\n", |
|
|
5540 |
" <td>0.608809</td>\n", |
|
|
5541 |
" <td>0.859970</td>\n", |
|
|
5542 |
" <td>0.531069</td>\n", |
|
|
5543 |
" <td>0.000000</td>\n", |
|
|
5544 |
" <td>0.000000</td>\n", |
|
|
5545 |
" <td>0.871844</td>\n", |
|
|
5546 |
" <td>0.000000</td>\n", |
|
|
5547 |
" <td>-0.286304</td>\n", |
|
|
5548 |
" <td>0.000000</td>\n", |
|
|
5549 |
" <td>0.000000</td>\n", |
|
|
5550 |
" <td>...</td>\n", |
|
|
5551 |
" <td>0.000000</td>\n", |
|
|
5552 |
" <td>-1.014500</td>\n", |
|
|
5553 |
" <td>-0.473931</td>\n", |
|
|
5554 |
" <td>0.000000</td>\n", |
|
|
5555 |
" <td>0.618239</td>\n", |
|
|
5556 |
" <td>0.000000</td>\n", |
|
|
5557 |
" <td>-0.386468</td>\n", |
|
|
5558 |
" <td>-1.494109</td>\n", |
|
|
5559 |
" <td>-0.312939</td>\n", |
|
|
5560 |
" <td>0.000000</td>\n", |
|
|
5561 |
" </tr>\n", |
|
|
5562 |
" <tr>\n", |
|
|
5563 |
" <th>642826</th>\n", |
|
|
5564 |
" <td>0.608809</td>\n", |
|
|
5565 |
" <td>0.859970</td>\n", |
|
|
5566 |
" <td>0.531069</td>\n", |
|
|
5567 |
" <td>0.000000</td>\n", |
|
|
5568 |
" <td>0.000000</td>\n", |
|
|
5569 |
" <td>0.871844</td>\n", |
|
|
5570 |
" <td>0.000000</td>\n", |
|
|
5571 |
" <td>-0.286304</td>\n", |
|
|
5572 |
" <td>0.000000</td>\n", |
|
|
5573 |
" <td>0.000000</td>\n", |
|
|
5574 |
" <td>...</td>\n", |
|
|
5575 |
" <td>0.000000</td>\n", |
|
|
5576 |
" <td>-1.014500</td>\n", |
|
|
5577 |
" <td>-0.473931</td>\n", |
|
|
5578 |
" <td>0.000000</td>\n", |
|
|
5579 |
" <td>0.618239</td>\n", |
|
|
5580 |
" <td>0.000000</td>\n", |
|
|
5581 |
" <td>-0.386468</td>\n", |
|
|
5582 |
" <td>-1.494109</td>\n", |
|
|
5583 |
" <td>-0.312939</td>\n", |
|
|
5584 |
" <td>0.000000</td>\n", |
|
|
5585 |
" </tr>\n", |
|
|
5586 |
" <tr>\n", |
|
|
5587 |
" <th>653067</th>\n", |
|
|
5588 |
" <td>0.000000</td>\n", |
|
|
5589 |
" <td>0.378512</td>\n", |
|
|
5590 |
" <td>0.000000</td>\n", |
|
|
5591 |
" <td>0.550901</td>\n", |
|
|
5592 |
" <td>0.000000</td>\n", |
|
|
5593 |
" <td>-0.434403</td>\n", |
|
|
5594 |
" <td>0.000000</td>\n", |
|
|
5595 |
" <td>-0.902389</td>\n", |
|
|
5596 |
" <td>1.220330</td>\n", |
|
|
5597 |
" <td>0.367371</td>\n", |
|
|
5598 |
" <td>...</td>\n", |
|
|
5599 |
" <td>0.000000</td>\n", |
|
|
5600 |
" <td>-1.014500</td>\n", |
|
|
5601 |
" <td>0.580145</td>\n", |
|
|
5602 |
" <td>0.000000</td>\n", |
|
|
5603 |
" <td>-1.014500</td>\n", |
|
|
5604 |
" <td>0.000000</td>\n", |
|
|
5605 |
" <td>0.000000</td>\n", |
|
|
5606 |
" <td>-0.577767</td>\n", |
|
|
5607 |
" <td>-1.494109</td>\n", |
|
|
5608 |
" <td>-1.494109</td>\n", |
|
|
5609 |
" </tr>\n", |
|
|
5610 |
" <tr>\n", |
|
|
5611 |
" <th>653067</th>\n", |
|
|
5612 |
" <td>0.000000</td>\n", |
|
|
5613 |
" <td>0.378512</td>\n", |
|
|
5614 |
" <td>0.000000</td>\n", |
|
|
5615 |
" <td>0.550901</td>\n", |
|
|
5616 |
" <td>0.000000</td>\n", |
|
|
5617 |
" <td>-0.434403</td>\n", |
|
|
5618 |
" <td>0.000000</td>\n", |
|
|
5619 |
" <td>-0.902389</td>\n", |
|
|
5620 |
" <td>1.220330</td>\n", |
|
|
5621 |
" <td>0.367371</td>\n", |
|
|
5622 |
" <td>...</td>\n", |
|
|
5623 |
" <td>0.000000</td>\n", |
|
|
5624 |
" <td>-1.014500</td>\n", |
|
|
5625 |
" <td>0.580145</td>\n", |
|
|
5626 |
" <td>0.000000</td>\n", |
|
|
5627 |
" <td>-1.014500</td>\n", |
|
|
5628 |
" <td>0.000000</td>\n", |
|
|
5629 |
" <td>0.000000</td>\n", |
|
|
5630 |
" <td>-0.577767</td>\n", |
|
|
5631 |
" <td>-1.494109</td>\n", |
|
|
5632 |
" <td>-1.494109</td>\n", |
|
|
5633 |
" </tr>\n", |
|
|
5634 |
" <tr>\n", |
|
|
5635 |
" <th>653067</th>\n", |
|
|
5636 |
" <td>0.000000</td>\n", |
|
|
5637 |
" <td>0.378512</td>\n", |
|
|
5638 |
" <td>0.000000</td>\n", |
|
|
5639 |
" <td>0.550901</td>\n", |
|
|
5640 |
" <td>0.000000</td>\n", |
|
|
5641 |
" <td>-0.434403</td>\n", |
|
|
5642 |
" <td>0.000000</td>\n", |
|
|
5643 |
" <td>-0.902389</td>\n", |
|
|
5644 |
" <td>1.220330</td>\n", |
|
|
5645 |
" <td>0.367371</td>\n", |
|
|
5646 |
" <td>...</td>\n", |
|
|
5647 |
" <td>0.000000</td>\n", |
|
|
5648 |
" <td>-1.014500</td>\n", |
|
|
5649 |
" <td>0.580145</td>\n", |
|
|
5650 |
" <td>0.000000</td>\n", |
|
|
5651 |
" <td>-1.014500</td>\n", |
|
|
5652 |
" <td>0.000000</td>\n", |
|
|
5653 |
" <td>0.000000</td>\n", |
|
|
5654 |
" <td>-0.577767</td>\n", |
|
|
5655 |
" <td>-1.494109</td>\n", |
|
|
5656 |
" <td>-1.494109</td>\n", |
|
|
5657 |
" </tr>\n", |
|
|
5658 |
" <tr>\n", |
|
|
5659 |
" <th>653067</th>\n", |
|
|
5660 |
" <td>0.000000</td>\n", |
|
|
5661 |
" <td>0.378512</td>\n", |
|
|
5662 |
" <td>0.000000</td>\n", |
|
|
5663 |
" <td>0.550901</td>\n", |
|
|
5664 |
" <td>0.000000</td>\n", |
|
|
5665 |
" <td>-0.434403</td>\n", |
|
|
5666 |
" <td>0.000000</td>\n", |
|
|
5667 |
" <td>-0.902389</td>\n", |
|
|
5668 |
" <td>1.220330</td>\n", |
|
|
5669 |
" <td>0.367371</td>\n", |
|
|
5670 |
" <td>...</td>\n", |
|
|
5671 |
" <td>0.000000</td>\n", |
|
|
5672 |
" <td>-1.014500</td>\n", |
|
|
5673 |
" <td>0.580145</td>\n", |
|
|
5674 |
" <td>0.000000</td>\n", |
|
|
5675 |
" <td>-1.014500</td>\n", |
|
|
5676 |
" <td>0.000000</td>\n", |
|
|
5677 |
" <td>0.000000</td>\n", |
|
|
5678 |
" <td>-0.577767</td>\n", |
|
|
5679 |
" <td>-1.494109</td>\n", |
|
|
5680 |
" <td>-1.494109</td>\n", |
|
|
5681 |
" </tr>\n", |
|
|
5682 |
" <tr>\n", |
|
|
5683 |
" <th>399761</th>\n", |
|
|
5684 |
" <td>0.531069</td>\n", |
|
|
5685 |
" <td>0.718088</td>\n", |
|
|
5686 |
" <td>0.000000</td>\n", |
|
|
5687 |
" <td>0.000000</td>\n", |
|
|
5688 |
" <td>0.000000</td>\n", |
|
|
5689 |
" <td>-0.251539</td>\n", |
|
|
5690 |
" <td>0.000000</td>\n", |
|
|
5691 |
" <td>-0.286304</td>\n", |
|
|
5692 |
" <td>0.000000</td>\n", |
|
|
5693 |
" <td>0.790772</td>\n", |
|
|
5694 |
" <td>...</td>\n", |
|
|
5695 |
" <td>0.367371</td>\n", |
|
|
5696 |
" <td>-1.535332</td>\n", |
|
|
5697 |
" <td>0.000000</td>\n", |
|
|
5698 |
" <td>0.000000</td>\n", |
|
|
5699 |
" <td>0.000000</td>\n", |
|
|
5700 |
" <td>0.000000</td>\n", |
|
|
5701 |
" <td>-0.599462</td>\n", |
|
|
5702 |
" <td>-0.588574</td>\n", |
|
|
5703 |
" <td>0.000000</td>\n", |
|
|
5704 |
" <td>0.000000</td>\n", |
|
|
5705 |
" </tr>\n", |
|
|
5706 |
" <tr>\n", |
|
|
5707 |
" <th>399761</th>\n", |
|
|
5708 |
" <td>0.531069</td>\n", |
|
|
5709 |
" <td>0.718088</td>\n", |
|
|
5710 |
" <td>0.000000</td>\n", |
|
|
5711 |
" <td>0.000000</td>\n", |
|
|
5712 |
" <td>0.000000</td>\n", |
|
|
5713 |
" <td>-0.251539</td>\n", |
|
|
5714 |
" <td>0.000000</td>\n", |
|
|
5715 |
" <td>-0.286304</td>\n", |
|
|
5716 |
" <td>0.000000</td>\n", |
|
|
5717 |
" <td>0.790772</td>\n", |
|
|
5718 |
" <td>...</td>\n", |
|
|
5719 |
" <td>0.367371</td>\n", |
|
|
5720 |
" <td>-1.535332</td>\n", |
|
|
5721 |
" <td>0.000000</td>\n", |
|
|
5722 |
" <td>0.000000</td>\n", |
|
|
5723 |
" <td>0.000000</td>\n", |
|
|
5724 |
" <td>0.000000</td>\n", |
|
|
5725 |
" <td>-0.599462</td>\n", |
|
|
5726 |
" <td>-0.588574</td>\n", |
|
|
5727 |
" <td>0.000000</td>\n", |
|
|
5728 |
" <td>0.000000</td>\n", |
|
|
5729 |
" </tr>\n", |
|
|
5730 |
" <tr>\n", |
|
|
5731 |
" <th>647060</th>\n", |
|
|
5732 |
" <td>0.000000</td>\n", |
|
|
5733 |
" <td>0.000000</td>\n", |
|
|
5734 |
" <td>0.000000</td>\n", |
|
|
5735 |
" <td>0.000000</td>\n", |
|
|
5736 |
" <td>0.000000</td>\n", |
|
|
5737 |
" <td>-0.312939</td>\n", |
|
|
5738 |
" <td>0.000000</td>\n", |
|
|
5739 |
" <td>-0.321928</td>\n", |
|
|
5740 |
" <td>0.000000</td>\n", |
|
|
5741 |
" <td>0.618239</td>\n", |
|
|
5742 |
" <td>...</td>\n", |
|
|
5743 |
" <td>0.000000</td>\n", |
|
|
5744 |
" <td>-0.621488</td>\n", |
|
|
5745 |
" <td>0.000000</td>\n", |
|
|
5746 |
" <td>-0.377070</td>\n", |
|
|
5747 |
" <td>-0.749038</td>\n", |
|
|
5748 |
" <td>-0.405451</td>\n", |
|
|
5749 |
" <td>0.000000</td>\n", |
|
|
5750 |
" <td>-0.395929</td>\n", |
|
|
5751 |
" <td>0.000000</td>\n", |
|
|
5752 |
" <td>0.000000</td>\n", |
|
|
5753 |
" </tr>\n", |
|
|
5754 |
" <tr>\n", |
|
|
5755 |
" <th>647060</th>\n", |
|
|
5756 |
" <td>0.000000</td>\n", |
|
|
5757 |
" <td>0.000000</td>\n", |
|
|
5758 |
" <td>0.000000</td>\n", |
|
|
5759 |
" <td>0.000000</td>\n", |
|
|
5760 |
" <td>0.000000</td>\n", |
|
|
5761 |
" <td>-0.312939</td>\n", |
|
|
5762 |
" <td>0.000000</td>\n", |
|
|
5763 |
" <td>-0.321928</td>\n", |
|
|
5764 |
" <td>0.000000</td>\n", |
|
|
5765 |
" <td>0.618239</td>\n", |
|
|
5766 |
" <td>...</td>\n", |
|
|
5767 |
" <td>0.000000</td>\n", |
|
|
5768 |
" <td>-0.621488</td>\n", |
|
|
5769 |
" <td>0.000000</td>\n", |
|
|
5770 |
" <td>-0.377070</td>\n", |
|
|
5771 |
" <td>-0.749038</td>\n", |
|
|
5772 |
" <td>-0.405451</td>\n", |
|
|
5773 |
" <td>0.000000</td>\n", |
|
|
5774 |
" <td>-0.395929</td>\n", |
|
|
5775 |
" <td>0.000000</td>\n", |
|
|
5776 |
" <td>0.000000</td>\n", |
|
|
5777 |
" </tr>\n", |
|
|
5778 |
" <tr>\n", |
|
|
5779 |
" <th>284565</th>\n", |
|
|
5780 |
" <td>1.238787</td>\n", |
|
|
5781 |
" <td>1.090853</td>\n", |
|
|
5782 |
" <td>0.000000</td>\n", |
|
|
5783 |
" <td>0.000000</td>\n", |
|
|
5784 |
" <td>0.000000</td>\n", |
|
|
5785 |
" <td>1.570463</td>\n", |
|
|
5786 |
" <td>0.000000</td>\n", |
|
|
5787 |
" <td>0.448901</td>\n", |
|
|
5788 |
" <td>0.411426</td>\n", |
|
|
5789 |
" <td>0.448901</td>\n", |
|
|
5790 |
" <td>...</td>\n", |
|
|
5791 |
" <td>0.469886</td>\n", |
|
|
5792 |
" <td>-0.504305</td>\n", |
|
|
5793 |
" <td>0.618239</td>\n", |
|
|
5794 |
" <td>0.201634</td>\n", |
|
|
5795 |
" <td>0.000000</td>\n", |
|
|
5796 |
" <td>-0.260152</td>\n", |
|
|
5797 |
" <td>0.000000</td>\n", |
|
|
5798 |
" <td>0.000000</td>\n", |
|
|
5799 |
" <td>0.469886</td>\n", |
|
|
5800 |
" <td>0.000000</td>\n", |
|
|
5801 |
" </tr>\n", |
|
|
5802 |
" <tr>\n", |
|
|
5803 |
" <th>284565</th>\n", |
|
|
5804 |
" <td>1.238787</td>\n", |
|
|
5805 |
" <td>1.090853</td>\n", |
|
|
5806 |
" <td>0.000000</td>\n", |
|
|
5807 |
" <td>0.000000</td>\n", |
|
|
5808 |
" <td>0.000000</td>\n", |
|
|
5809 |
" <td>1.310340</td>\n", |
|
|
5810 |
" <td>0.000000</td>\n", |
|
|
5811 |
" <td>0.448901</td>\n", |
|
|
5812 |
" <td>0.411426</td>\n", |
|
|
5813 |
" <td>0.448901</td>\n", |
|
|
5814 |
" <td>...</td>\n", |
|
|
5815 |
" <td>0.469886</td>\n", |
|
|
5816 |
" <td>-0.524915</td>\n", |
|
|
5817 |
" <td>0.618239</td>\n", |
|
|
5818 |
" <td>0.201634</td>\n", |
|
|
5819 |
" <td>0.000000</td>\n", |
|
|
5820 |
" <td>-0.260152</td>\n", |
|
|
5821 |
" <td>0.000000</td>\n", |
|
|
5822 |
" <td>0.000000</td>\n", |
|
|
5823 |
" <td>0.469886</td>\n", |
|
|
5824 |
" <td>0.000000</td>\n", |
|
|
5825 |
" </tr>\n", |
|
|
5826 |
" <tr>\n", |
|
|
5827 |
" <th>84631</th>\n", |
|
|
5828 |
" <td>-0.823677</td>\n", |
|
|
5829 |
" <td>-0.524915</td>\n", |
|
|
5830 |
" <td>0.000000</td>\n", |
|
|
5831 |
" <td>0.632268</td>\n", |
|
|
5832 |
" <td>0.000000</td>\n", |
|
|
5833 |
" <td>-1.074001</td>\n", |
|
|
5834 |
" <td>0.000000</td>\n", |
|
|
5835 |
" <td>-0.875672</td>\n", |
|
|
5836 |
" <td>-0.678072</td>\n", |
|
|
5837 |
" <td>0.378512</td>\n", |
|
|
5838 |
" <td>...</td>\n", |
|
|
5839 |
" <td>0.000000</td>\n", |
|
|
5840 |
" <td>-1.014500</td>\n", |
|
|
5841 |
" <td>0.500802</td>\n", |
|
|
5842 |
" <td>0.000000</td>\n", |
|
|
5843 |
" <td>0.000000</td>\n", |
|
|
5844 |
" <td>0.000000</td>\n", |
|
|
5845 |
" <td>0.000000</td>\n", |
|
|
5846 |
" <td>-0.545824</td>\n", |
|
|
5847 |
" <td>-0.545824</td>\n", |
|
|
5848 |
" <td>-0.535332</td>\n", |
|
|
5849 |
" </tr>\n", |
|
|
5850 |
" <tr>\n", |
|
|
5851 |
" <th>84631</th>\n", |
|
|
5852 |
" <td>-0.823677</td>\n", |
|
|
5853 |
" <td>-0.524915</td>\n", |
|
|
5854 |
" <td>0.000000</td>\n", |
|
|
5855 |
" <td>0.632268</td>\n", |
|
|
5856 |
" <td>0.000000</td>\n", |
|
|
5857 |
" <td>-1.074001</td>\n", |
|
|
5858 |
" <td>0.000000</td>\n", |
|
|
5859 |
" <td>-0.875672</td>\n", |
|
|
5860 |
" <td>-0.678072</td>\n", |
|
|
5861 |
" <td>0.378512</td>\n", |
|
|
5862 |
" <td>...</td>\n", |
|
|
5863 |
" <td>0.000000</td>\n", |
|
|
5864 |
" <td>-1.014500</td>\n", |
|
|
5865 |
" <td>0.500802</td>\n", |
|
|
5866 |
" <td>0.000000</td>\n", |
|
|
5867 |
" <td>0.000000</td>\n", |
|
|
5868 |
" <td>0.000000</td>\n", |
|
|
5869 |
" <td>0.000000</td>\n", |
|
|
5870 |
" <td>-0.545824</td>\n", |
|
|
5871 |
" <td>-0.545824</td>\n", |
|
|
5872 |
" <td>-0.535332</td>\n", |
|
|
5873 |
" </tr>\n", |
|
|
5874 |
" <tr>\n", |
|
|
5875 |
" <th>161176</th>\n", |
|
|
5876 |
" <td>0.000000</td>\n", |
|
|
5877 |
" <td>0.000000</td>\n", |
|
|
5878 |
" <td>0.000000</td>\n", |
|
|
5879 |
" <td>0.000000</td>\n", |
|
|
5880 |
" <td>0.000000</td>\n", |
|
|
5881 |
" <td>0.000000</td>\n", |
|
|
5882 |
" <td>0.000000</td>\n", |
|
|
5883 |
" <td>-0.358454</td>\n", |
|
|
5884 |
" <td>0.250962</td>\n", |
|
|
5885 |
" <td>0.339137</td>\n", |
|
|
5886 |
" <td>...</td>\n", |
|
|
5887 |
" <td>-0.875672</td>\n", |
|
|
5888 |
" <td>0.000000</td>\n", |
|
|
5889 |
" <td>-0.483985</td>\n", |
|
|
5890 |
" <td>0.000000</td>\n", |
|
|
5891 |
" <td>0.000000</td>\n", |
|
|
5892 |
" <td>-0.610433</td>\n", |
|
|
5893 |
" <td>0.000000</td>\n", |
|
|
5894 |
" <td>0.411426</td>\n", |
|
|
5895 |
" <td>0.000000</td>\n", |
|
|
5896 |
" <td>0.000000</td>\n", |
|
|
5897 |
" </tr>\n", |
|
|
5898 |
" <tr>\n", |
|
|
5899 |
" <th>161176</th>\n", |
|
|
5900 |
" <td>0.000000</td>\n", |
|
|
5901 |
" <td>0.000000</td>\n", |
|
|
5902 |
" <td>0.000000</td>\n", |
|
|
5903 |
" <td>0.000000</td>\n", |
|
|
5904 |
" <td>0.000000</td>\n", |
|
|
5905 |
" <td>0.000000</td>\n", |
|
|
5906 |
" <td>0.000000</td>\n", |
|
|
5907 |
" <td>-0.358454</td>\n", |
|
|
5908 |
" <td>0.250962</td>\n", |
|
|
5909 |
" <td>0.339137</td>\n", |
|
|
5910 |
" <td>...</td>\n", |
|
|
5911 |
" <td>-0.875672</td>\n", |
|
|
5912 |
" <td>0.000000</td>\n", |
|
|
5913 |
" <td>-0.483985</td>\n", |
|
|
5914 |
" <td>0.000000</td>\n", |
|
|
5915 |
" <td>0.000000</td>\n", |
|
|
5916 |
" <td>-0.610433</td>\n", |
|
|
5917 |
" <td>0.000000</td>\n", |
|
|
5918 |
" <td>0.411426</td>\n", |
|
|
5919 |
" <td>0.000000</td>\n", |
|
|
5920 |
" <td>0.000000</td>\n", |
|
|
5921 |
" </tr>\n", |
|
|
5922 |
" <tr>\n", |
|
|
5923 |
" <th>341019</th>\n", |
|
|
5924 |
" <td>0.959770</td>\n", |
|
|
5925 |
" <td>0.000000</td>\n", |
|
|
5926 |
" <td>0.000000</td>\n", |
|
|
5927 |
" <td>0.000000</td>\n", |
|
|
5928 |
" <td>0.000000</td>\n", |
|
|
5929 |
" <td>-0.304006</td>\n", |
|
|
5930 |
" <td>0.000000</td>\n", |
|
|
5931 |
" <td>-0.349235</td>\n", |
|
|
5932 |
" <td>0.000000</td>\n", |
|
|
5933 |
" <td>0.000000</td>\n", |
|
|
5934 |
" <td>...</td>\n", |
|
|
5935 |
" <td>0.000000</td>\n", |
|
|
5936 |
" <td>-0.666576</td>\n", |
|
|
5937 |
" <td>0.000000</td>\n", |
|
|
5938 |
" <td>-0.304006</td>\n", |
|
|
5939 |
" <td>-1.000000</td>\n", |
|
|
5940 |
" <td>-0.610433</td>\n", |
|
|
5941 |
" <td>0.000000</td>\n", |
|
|
5942 |
" <td>0.000000</td>\n", |
|
|
5943 |
" <td>-0.444184</td>\n", |
|
|
5944 |
" <td>0.000000</td>\n", |
|
|
5945 |
" </tr>\n", |
|
|
5946 |
" <tr>\n", |
|
|
5947 |
" <th>341019</th>\n", |
|
|
5948 |
" <td>0.959770</td>\n", |
|
|
5949 |
" <td>0.000000</td>\n", |
|
|
5950 |
" <td>0.000000</td>\n", |
|
|
5951 |
" <td>0.000000</td>\n", |
|
|
5952 |
" <td>0.000000</td>\n", |
|
|
5953 |
" <td>-0.304006</td>\n", |
|
|
5954 |
" <td>0.000000</td>\n", |
|
|
5955 |
" <td>-0.349235</td>\n", |
|
|
5956 |
" <td>0.000000</td>\n", |
|
|
5957 |
" <td>0.000000</td>\n", |
|
|
5958 |
" <td>...</td>\n", |
|
|
5959 |
" <td>0.000000</td>\n", |
|
|
5960 |
" <td>-0.312939</td>\n", |
|
|
5961 |
" <td>0.000000</td>\n", |
|
|
5962 |
" <td>-0.304006</td>\n", |
|
|
5963 |
" <td>-1.000000</td>\n", |
|
|
5964 |
" <td>-0.610433</td>\n", |
|
|
5965 |
" <td>0.000000</td>\n", |
|
|
5966 |
" <td>0.000000</td>\n", |
|
|
5967 |
" <td>-0.444184</td>\n", |
|
|
5968 |
" <td>0.000000</td>\n", |
|
|
5969 |
" </tr>\n", |
|
|
5970 |
" <tr>\n", |
|
|
5971 |
" <th>83869</th>\n", |
|
|
5972 |
" <td>-3.000000</td>\n", |
|
|
5973 |
" <td>-3.184425</td>\n", |
|
|
5974 |
" <td>-3.321928</td>\n", |
|
|
5975 |
" <td>-3.000000</td>\n", |
|
|
5976 |
" <td>-2.599462</td>\n", |
|
|
5977 |
" <td>-3.556393</td>\n", |
|
|
5978 |
" <td>-2.785875</td>\n", |
|
|
5979 |
" <td>-0.875672</td>\n", |
|
|
5980 |
" <td>-2.736966</td>\n", |
|
|
5981 |
" <td>-2.514573</td>\n", |
|
|
5982 |
" <td>...</td>\n", |
|
|
5983 |
" <td>-2.556393</td>\n", |
|
|
5984 |
" <td>-3.943416</td>\n", |
|
|
5985 |
" <td>-2.785875</td>\n", |
|
|
5986 |
" <td>-2.152003</td>\n", |
|
|
5987 |
" <td>-3.556393</td>\n", |
|
|
5988 |
" <td>-3.251539</td>\n", |
|
|
5989 |
" <td>-2.736966</td>\n", |
|
|
5990 |
" <td>-3.473931</td>\n", |
|
|
5991 |
" <td>-3.120294</td>\n", |
|
|
5992 |
" <td>-3.643856</td>\n", |
|
|
5993 |
" </tr>\n", |
|
|
5994 |
" <tr>\n", |
|
|
5995 |
" <th>83869</th>\n", |
|
|
5996 |
" <td>-3.000000</td>\n", |
|
|
5997 |
" <td>-3.184425</td>\n", |
|
|
5998 |
" <td>-3.321928</td>\n", |
|
|
5999 |
" <td>-3.000000</td>\n", |
|
|
6000 |
" <td>-2.599462</td>\n", |
|
|
6001 |
" <td>-3.556393</td>\n", |
|
|
6002 |
" <td>-2.785875</td>\n", |
|
|
6003 |
" <td>-0.875672</td>\n", |
|
|
6004 |
" <td>-2.736966</td>\n", |
|
|
6005 |
" <td>-2.514573</td>\n", |
|
|
6006 |
" <td>...</td>\n", |
|
|
6007 |
" <td>-2.556393</td>\n", |
|
|
6008 |
" <td>-3.943416</td>\n", |
|
|
6009 |
" <td>-2.785875</td>\n", |
|
|
6010 |
" <td>-2.152003</td>\n", |
|
|
6011 |
" <td>-3.556393</td>\n", |
|
|
6012 |
" <td>-3.251539</td>\n", |
|
|
6013 |
" <td>-2.736966</td>\n", |
|
|
6014 |
" <td>-3.473931</td>\n", |
|
|
6015 |
" <td>-3.120294</td>\n", |
|
|
6016 |
" <td>-3.643856</td>\n", |
|
|
6017 |
" </tr>\n", |
|
|
6018 |
" <tr>\n", |
|
|
6019 |
" <th>9502</th>\n", |
|
|
6020 |
" <td>0.000000</td>\n", |
|
|
6021 |
" <td>0.378512</td>\n", |
|
|
6022 |
" <td>0.000000</td>\n", |
|
|
6023 |
" <td>0.550901</td>\n", |
|
|
6024 |
" <td>0.000000</td>\n", |
|
|
6025 |
" <td>-0.434403</td>\n", |
|
|
6026 |
" <td>0.000000</td>\n", |
|
|
6027 |
" <td>-0.902389</td>\n", |
|
|
6028 |
" <td>1.220330</td>\n", |
|
|
6029 |
" <td>0.367371</td>\n", |
|
|
6030 |
" <td>...</td>\n", |
|
|
6031 |
" <td>0.000000</td>\n", |
|
|
6032 |
" <td>-1.014500</td>\n", |
|
|
6033 |
" <td>0.580145</td>\n", |
|
|
6034 |
" <td>0.000000</td>\n", |
|
|
6035 |
" <td>-1.014500</td>\n", |
|
|
6036 |
" <td>0.000000</td>\n", |
|
|
6037 |
" <td>0.000000</td>\n", |
|
|
6038 |
" <td>-0.577767</td>\n", |
|
|
6039 |
" <td>-1.494109</td>\n", |
|
|
6040 |
" <td>-1.494109</td>\n", |
|
|
6041 |
" </tr>\n", |
|
|
6042 |
" <tr>\n", |
|
|
6043 |
" <th>9502</th>\n", |
|
|
6044 |
" <td>0.000000</td>\n", |
|
|
6045 |
" <td>0.378512</td>\n", |
|
|
6046 |
" <td>0.000000</td>\n", |
|
|
6047 |
" <td>0.550901</td>\n", |
|
|
6048 |
" <td>0.000000</td>\n", |
|
|
6049 |
" <td>-0.434403</td>\n", |
|
|
6050 |
" <td>0.000000</td>\n", |
|
|
6051 |
" <td>-0.902389</td>\n", |
|
|
6052 |
" <td>1.220330</td>\n", |
|
|
6053 |
" <td>0.367371</td>\n", |
|
|
6054 |
" <td>...</td>\n", |
|
|
6055 |
" <td>0.000000</td>\n", |
|
|
6056 |
" <td>-1.014500</td>\n", |
|
|
6057 |
" <td>0.580145</td>\n", |
|
|
6058 |
" <td>0.000000</td>\n", |
|
|
6059 |
" <td>-1.014500</td>\n", |
|
|
6060 |
" <td>0.000000</td>\n", |
|
|
6061 |
" <td>0.000000</td>\n", |
|
|
6062 |
" <td>-0.577767</td>\n", |
|
|
6063 |
" <td>-1.494109</td>\n", |
|
|
6064 |
" <td>-1.494109</td>\n", |
|
|
6065 |
" </tr>\n", |
|
|
6066 |
" <tr>\n", |
|
|
6067 |
" <th>83871</th>\n", |
|
|
6068 |
" <td>0.000000</td>\n", |
|
|
6069 |
" <td>0.000000</td>\n", |
|
|
6070 |
" <td>0.000000</td>\n", |
|
|
6071 |
" <td>0.500802</td>\n", |
|
|
6072 |
" <td>0.000000</td>\n", |
|
|
6073 |
" <td>-0.304006</td>\n", |
|
|
6074 |
" <td>0.000000</td>\n", |
|
|
6075 |
" <td>-0.349235</td>\n", |
|
|
6076 |
" <td>0.327687</td>\n", |
|
|
6077 |
" <td>0.000000</td>\n", |
|
|
6078 |
" <td>...</td>\n", |
|
|
6079 |
" <td>0.000000</td>\n", |
|
|
6080 |
" <td>0.000000</td>\n", |
|
|
6081 |
" <td>-0.463947</td>\n", |
|
|
6082 |
" <td>-0.358454</td>\n", |
|
|
6083 |
" <td>0.000000</td>\n", |
|
|
6084 |
" <td>0.000000</td>\n", |
|
|
6085 |
" <td>0.000000</td>\n", |
|
|
6086 |
" <td>0.448901</td>\n", |
|
|
6087 |
" <td>-0.535332</td>\n", |
|
|
6088 |
" <td>0.000000</td>\n", |
|
|
6089 |
" </tr>\n", |
|
|
6090 |
" <tr>\n", |
|
|
6091 |
" <th>...</th>\n", |
|
|
6092 |
" <td>...</td>\n", |
|
|
6093 |
" <td>...</td>\n", |
|
|
6094 |
" <td>...</td>\n", |
|
|
6095 |
" <td>...</td>\n", |
|
|
6096 |
" <td>...</td>\n", |
|
|
6097 |
" <td>...</td>\n", |
|
|
6098 |
" <td>...</td>\n", |
|
|
6099 |
" <td>...</td>\n", |
|
|
6100 |
" <td>...</td>\n", |
|
|
6101 |
" <td>...</td>\n", |
|
|
6102 |
" <td>...</td>\n", |
|
|
6103 |
" <td>...</td>\n", |
|
|
6104 |
" <td>...</td>\n", |
|
|
6105 |
" <td>...</td>\n", |
|
|
6106 |
" <td>...</td>\n", |
|
|
6107 |
" <td>...</td>\n", |
|
|
6108 |
" <td>...</td>\n", |
|
|
6109 |
" <td>...</td>\n", |
|
|
6110 |
" <td>...</td>\n", |
|
|
6111 |
" <td>...</td>\n", |
|
|
6112 |
" <td>...</td>\n", |
|
|
6113 |
" </tr>\n", |
|
|
6114 |
" <tr>\n", |
|
|
6115 |
" <th>100134869</th>\n", |
|
|
6116 |
" <td>0.000000</td>\n", |
|
|
6117 |
" <td>0.207893</td>\n", |
|
|
6118 |
" <td>0.000000</td>\n", |
|
|
6119 |
" <td>0.000000</td>\n", |
|
|
6120 |
" <td>0.000000</td>\n", |
|
|
6121 |
" <td>0.000000</td>\n", |
|
|
6122 |
" <td>0.000000</td>\n", |
|
|
6123 |
" <td>0.000000</td>\n", |
|
|
6124 |
" <td>0.232661</td>\n", |
|
|
6125 |
" <td>0.000000</td>\n", |
|
|
6126 |
" <td>...</td>\n", |
|
|
6127 |
" <td>0.000000</td>\n", |
|
|
6128 |
" <td>0.389567</td>\n", |
|
|
6129 |
" <td>0.000000</td>\n", |
|
|
6130 |
" <td>0.000000</td>\n", |
|
|
6131 |
" <td>-0.463947</td>\n", |
|
|
6132 |
" <td>0.000000</td>\n", |
|
|
6133 |
" <td>-0.367732</td>\n", |
|
|
6134 |
" <td>0.790772</td>\n", |
|
|
6135 |
" <td>0.000000</td>\n", |
|
|
6136 |
" <td>-0.535332</td>\n", |
|
|
6137 |
" </tr>\n", |
|
|
6138 |
" <tr>\n", |
|
|
6139 |
" <th>100134869</th>\n", |
|
|
6140 |
" <td>0.000000</td>\n", |
|
|
6141 |
" <td>0.207893</td>\n", |
|
|
6142 |
" <td>0.000000</td>\n", |
|
|
6143 |
" <td>0.000000</td>\n", |
|
|
6144 |
" <td>0.000000</td>\n", |
|
|
6145 |
" <td>0.000000</td>\n", |
|
|
6146 |
" <td>0.000000</td>\n", |
|
|
6147 |
" <td>0.000000</td>\n", |
|
|
6148 |
" <td>0.232661</td>\n", |
|
|
6149 |
" <td>0.000000</td>\n", |
|
|
6150 |
" <td>...</td>\n", |
|
|
6151 |
" <td>0.000000</td>\n", |
|
|
6152 |
" <td>0.389567</td>\n", |
|
|
6153 |
" <td>0.000000</td>\n", |
|
|
6154 |
" <td>0.000000</td>\n", |
|
|
6155 |
" <td>-0.463947</td>\n", |
|
|
6156 |
" <td>0.000000</td>\n", |
|
|
6157 |
" <td>-0.367732</td>\n", |
|
|
6158 |
" <td>0.790772</td>\n", |
|
|
6159 |
" <td>0.000000</td>\n", |
|
|
6160 |
" <td>-0.535332</td>\n", |
|
|
6161 |
" </tr>\n", |
|
|
6162 |
" <tr>\n", |
|
|
6163 |
" <th>84316</th>\n", |
|
|
6164 |
" <td>-0.251539</td>\n", |
|
|
6165 |
" <td>0.000000</td>\n", |
|
|
6166 |
" <td>0.000000</td>\n", |
|
|
6167 |
" <td>0.000000</td>\n", |
|
|
6168 |
" <td>0.000000</td>\n", |
|
|
6169 |
" <td>-0.340075</td>\n", |
|
|
6170 |
" <td>0.000000</td>\n", |
|
|
6171 |
" <td>-0.349235</td>\n", |
|
|
6172 |
" <td>-0.588574</td>\n", |
|
|
6173 |
" <td>0.000000</td>\n", |
|
|
6174 |
" <td>...</td>\n", |
|
|
6175 |
" <td>0.000000</td>\n", |
|
|
6176 |
" <td>-0.985645</td>\n", |
|
|
6177 |
" <td>-0.358454</td>\n", |
|
|
6178 |
" <td>-0.340075</td>\n", |
|
|
6179 |
" <td>-0.971431</td>\n", |
|
|
6180 |
" <td>-0.545824</td>\n", |
|
|
6181 |
" <td>0.310340</td>\n", |
|
|
6182 |
" <td>0.438293</td>\n", |
|
|
6183 |
" <td>-0.473931</td>\n", |
|
|
6184 |
" <td>0.000000</td>\n", |
|
|
6185 |
" </tr>\n", |
|
|
6186 |
" <tr>\n", |
|
|
6187 |
" <th>84316</th>\n", |
|
|
6188 |
" <td>-0.810966</td>\n", |
|
|
6189 |
" <td>-0.689660</td>\n", |
|
|
6190 |
" <td>0.000000</td>\n", |
|
|
6191 |
" <td>0.000000</td>\n", |
|
|
6192 |
" <td>0.000000</td>\n", |
|
|
6193 |
" <td>0.718088</td>\n", |
|
|
6194 |
" <td>0.000000</td>\n", |
|
|
6195 |
" <td>0.000000</td>\n", |
|
|
6196 |
" <td>0.731183</td>\n", |
|
|
6197 |
" <td>0.367371</td>\n", |
|
|
6198 |
" <td>...</td>\n", |
|
|
6199 |
" <td>0.000000</td>\n", |
|
|
6200 |
" <td>0.000000</td>\n", |
|
|
6201 |
" <td>0.000000</td>\n", |
|
|
6202 |
" <td>-0.434403</td>\n", |
|
|
6203 |
" <td>1.060047</td>\n", |
|
|
6204 |
" <td>0.490570</td>\n", |
|
|
6205 |
" <td>0.000000</td>\n", |
|
|
6206 |
" <td>-0.632629</td>\n", |
|
|
6207 |
" <td>-0.655172</td>\n", |
|
|
6208 |
" <td>0.000000</td>\n", |
|
|
6209 |
" </tr>\n", |
|
|
6210 |
" <tr>\n", |
|
|
6211 |
" <th>200030</th>\n", |
|
|
6212 |
" <td>1.238787</td>\n", |
|
|
6213 |
" <td>1.090853</td>\n", |
|
|
6214 |
" <td>0.000000</td>\n", |
|
|
6215 |
" <td>0.000000</td>\n", |
|
|
6216 |
" <td>0.000000</td>\n", |
|
|
6217 |
" <td>1.839960</td>\n", |
|
|
6218 |
" <td>0.000000</td>\n", |
|
|
6219 |
" <td>0.448901</td>\n", |
|
|
6220 |
" <td>0.000000</td>\n", |
|
|
6221 |
" <td>0.000000</td>\n", |
|
|
6222 |
" <td>...</td>\n", |
|
|
6223 |
" <td>0.438293</td>\n", |
|
|
6224 |
" <td>0.000000</td>\n", |
|
|
6225 |
" <td>0.618239</td>\n", |
|
|
6226 |
" <td>0.201634</td>\n", |
|
|
6227 |
" <td>0.000000</td>\n", |
|
|
6228 |
" <td>-0.260152</td>\n", |
|
|
6229 |
" <td>0.000000</td>\n", |
|
|
6230 |
" <td>0.000000</td>\n", |
|
|
6231 |
" <td>0.469886</td>\n", |
|
|
6232 |
" <td>0.000000</td>\n", |
|
|
6233 |
" </tr>\n", |
|
|
6234 |
" <tr>\n", |
|
|
6235 |
" <th>200030</th>\n", |
|
|
6236 |
" <td>1.238787</td>\n", |
|
|
6237 |
" <td>1.090853</td>\n", |
|
|
6238 |
" <td>0.000000</td>\n", |
|
|
6239 |
" <td>0.000000</td>\n", |
|
|
6240 |
" <td>0.000000</td>\n", |
|
|
6241 |
" <td>1.839960</td>\n", |
|
|
6242 |
" <td>0.000000</td>\n", |
|
|
6243 |
" <td>0.448901</td>\n", |
|
|
6244 |
" <td>0.000000</td>\n", |
|
|
6245 |
" <td>0.000000</td>\n", |
|
|
6246 |
" <td>...</td>\n", |
|
|
6247 |
" <td>0.438293</td>\n", |
|
|
6248 |
" <td>0.000000</td>\n", |
|
|
6249 |
" <td>0.618239</td>\n", |
|
|
6250 |
" <td>0.201634</td>\n", |
|
|
6251 |
" <td>0.000000</td>\n", |
|
|
6252 |
" <td>-0.260152</td>\n", |
|
|
6253 |
" <td>0.000000</td>\n", |
|
|
6254 |
" <td>0.000000</td>\n", |
|
|
6255 |
" <td>0.469886</td>\n", |
|
|
6256 |
" <td>0.000000</td>\n", |
|
|
6257 |
" </tr>\n", |
|
|
6258 |
" <tr>\n", |
|
|
6259 |
" <th>642658</th>\n", |
|
|
6260 |
" <td>1.049631</td>\n", |
|
|
6261 |
" <td>1.358959</td>\n", |
|
|
6262 |
" <td>0.000000</td>\n", |
|
|
6263 |
" <td>0.599318</td>\n", |
|
|
6264 |
" <td>0.000000</td>\n", |
|
|
6265 |
" <td>0.000000</td>\n", |
|
|
6266 |
" <td>0.000000</td>\n", |
|
|
6267 |
" <td>0.321928</td>\n", |
|
|
6268 |
" <td>0.700440</td>\n", |
|
|
6269 |
" <td>0.298658</td>\n", |
|
|
6270 |
" <td>...</td>\n", |
|
|
6271 |
" <td>0.632268</td>\n", |
|
|
6272 |
" <td>0.000000</td>\n", |
|
|
6273 |
" <td>0.769772</td>\n", |
|
|
6274 |
" <td>0.232661</td>\n", |
|
|
6275 |
" <td>1.121015</td>\n", |
|
|
6276 |
" <td>0.831877</td>\n", |
|
|
6277 |
" <td>-0.367732</td>\n", |
|
|
6278 |
" <td>0.000000</td>\n", |
|
|
6279 |
" <td>1.121015</td>\n", |
|
|
6280 |
" <td>0.459432</td>\n", |
|
|
6281 |
" </tr>\n", |
|
|
6282 |
" <tr>\n", |
|
|
6283 |
" <th>642658</th>\n", |
|
|
6284 |
" <td>1.049631</td>\n", |
|
|
6285 |
" <td>1.358959</td>\n", |
|
|
6286 |
" <td>0.000000</td>\n", |
|
|
6287 |
" <td>0.599318</td>\n", |
|
|
6288 |
" <td>0.000000</td>\n", |
|
|
6289 |
" <td>0.000000</td>\n", |
|
|
6290 |
" <td>0.000000</td>\n", |
|
|
6291 |
" <td>0.321928</td>\n", |
|
|
6292 |
" <td>0.700440</td>\n", |
|
|
6293 |
" <td>0.298658</td>\n", |
|
|
6294 |
" <td>...</td>\n", |
|
|
6295 |
" <td>0.632268</td>\n", |
|
|
6296 |
" <td>0.000000</td>\n", |
|
|
6297 |
" <td>0.769772</td>\n", |
|
|
6298 |
" <td>0.232661</td>\n", |
|
|
6299 |
" <td>1.121015</td>\n", |
|
|
6300 |
" <td>0.831877</td>\n", |
|
|
6301 |
" <td>-0.367732</td>\n", |
|
|
6302 |
" <td>0.000000</td>\n", |
|
|
6303 |
" <td>1.121015</td>\n", |
|
|
6304 |
" <td>0.459432</td>\n", |
|
|
6305 |
" </tr>\n", |
|
|
6306 |
" <tr>\n", |
|
|
6307 |
" <th>100302179</th>\n", |
|
|
6308 |
" <td>0.778209</td>\n", |
|
|
6309 |
" <td>0.000000</td>\n", |
|
|
6310 |
" <td>0.000000</td>\n", |
|
|
6311 |
" <td>0.000000</td>\n", |
|
|
6312 |
" <td>0.000000</td>\n", |
|
|
6313 |
" <td>-0.340075</td>\n", |
|
|
6314 |
" <td>0.000000</td>\n", |
|
|
6315 |
" <td>0.000000</td>\n", |
|
|
6316 |
" <td>0.000000</td>\n", |
|
|
6317 |
" <td>0.000000</td>\n", |
|
|
6318 |
" <td>...</td>\n", |
|
|
6319 |
" <td>0.000000</td>\n", |
|
|
6320 |
" <td>0.000000</td>\n", |
|
|
6321 |
" <td>0.201634</td>\n", |
|
|
6322 |
" <td>-0.251539</td>\n", |
|
|
6323 |
" <td>0.000000</td>\n", |
|
|
6324 |
" <td>-0.463947</td>\n", |
|
|
6325 |
" <td>0.000000</td>\n", |
|
|
6326 |
" <td>0.000000</td>\n", |
|
|
6327 |
" <td>0.000000</td>\n", |
|
|
6328 |
" <td>0.000000</td>\n", |
|
|
6329 |
" </tr>\n", |
|
|
6330 |
" <tr>\n", |
|
|
6331 |
" <th>100302179</th>\n", |
|
|
6332 |
" <td>0.778209</td>\n", |
|
|
6333 |
" <td>0.000000</td>\n", |
|
|
6334 |
" <td>0.000000</td>\n", |
|
|
6335 |
" <td>0.000000</td>\n", |
|
|
6336 |
" <td>0.000000</td>\n", |
|
|
6337 |
" <td>-0.340075</td>\n", |
|
|
6338 |
" <td>0.000000</td>\n", |
|
|
6339 |
" <td>0.000000</td>\n", |
|
|
6340 |
" <td>0.000000</td>\n", |
|
|
6341 |
" <td>0.000000</td>\n", |
|
|
6342 |
" <td>...</td>\n", |
|
|
6343 |
" <td>0.000000</td>\n", |
|
|
6344 |
" <td>0.000000</td>\n", |
|
|
6345 |
" <td>0.201634</td>\n", |
|
|
6346 |
" <td>-0.251539</td>\n", |
|
|
6347 |
" <td>0.000000</td>\n", |
|
|
6348 |
" <td>-0.463947</td>\n", |
|
|
6349 |
" <td>0.000000</td>\n", |
|
|
6350 |
" <td>0.000000</td>\n", |
|
|
6351 |
" <td>0.000000</td>\n", |
|
|
6352 |
" <td>0.000000</td>\n", |
|
|
6353 |
" </tr>\n", |
|
|
6354 |
" <tr>\n", |
|
|
6355 |
" <th>401508</th>\n", |
|
|
6356 |
" <td>0.232661</td>\n", |
|
|
6357 |
" <td>0.000000</td>\n", |
|
|
6358 |
" <td>0.000000</td>\n", |
|
|
6359 |
" <td>0.000000</td>\n", |
|
|
6360 |
" <td>0.250962</td>\n", |
|
|
6361 |
" <td>0.000000</td>\n", |
|
|
6362 |
" <td>0.207893</td>\n", |
|
|
6363 |
" <td>0.000000</td>\n", |
|
|
6364 |
" <td>-0.666576</td>\n", |
|
|
6365 |
" <td>1.629939</td>\n", |
|
|
6366 |
" <td>...</td>\n", |
|
|
6367 |
" <td>0.000000</td>\n", |
|
|
6368 |
" <td>-2.321928</td>\n", |
|
|
6369 |
" <td>0.000000</td>\n", |
|
|
6370 |
" <td>0.000000</td>\n", |
|
|
6371 |
" <td>-0.260152</td>\n", |
|
|
6372 |
" <td>0.000000</td>\n", |
|
|
6373 |
" <td>-0.545824</td>\n", |
|
|
6374 |
" <td>-0.330973</td>\n", |
|
|
6375 |
" <td>0.000000</td>\n", |
|
|
6376 |
" <td>0.000000</td>\n", |
|
|
6377 |
" </tr>\n", |
|
|
6378 |
" <tr>\n", |
|
|
6379 |
" <th>401508</th>\n", |
|
|
6380 |
" <td>0.232661</td>\n", |
|
|
6381 |
" <td>0.000000</td>\n", |
|
|
6382 |
" <td>0.000000</td>\n", |
|
|
6383 |
" <td>0.000000</td>\n", |
|
|
6384 |
" <td>0.250962</td>\n", |
|
|
6385 |
" <td>0.000000</td>\n", |
|
|
6386 |
" <td>0.207893</td>\n", |
|
|
6387 |
" <td>0.000000</td>\n", |
|
|
6388 |
" <td>-0.666576</td>\n", |
|
|
6389 |
" <td>1.629939</td>\n", |
|
|
6390 |
" <td>...</td>\n", |
|
|
6391 |
" <td>0.000000</td>\n", |
|
|
6392 |
" <td>-2.321928</td>\n", |
|
|
6393 |
" <td>0.000000</td>\n", |
|
|
6394 |
" <td>0.000000</td>\n", |
|
|
6395 |
" <td>-0.260152</td>\n", |
|
|
6396 |
" <td>0.000000</td>\n", |
|
|
6397 |
" <td>-0.545824</td>\n", |
|
|
6398 |
" <td>-0.330973</td>\n", |
|
|
6399 |
" <td>0.000000</td>\n", |
|
|
6400 |
" <td>0.000000</td>\n", |
|
|
6401 |
" </tr>\n", |
|
|
6402 |
" <tr>\n", |
|
|
6403 |
" <th>119016</th>\n", |
|
|
6404 |
" <td>0.378512</td>\n", |
|
|
6405 |
" <td>0.570463</td>\n", |
|
|
6406 |
" <td>0.000000</td>\n", |
|
|
6407 |
" <td>0.000000</td>\n", |
|
|
6408 |
" <td>0.000000</td>\n", |
|
|
6409 |
" <td>-0.251539</td>\n", |
|
|
6410 |
" <td>0.000000</td>\n", |
|
|
6411 |
" <td>-0.286304</td>\n", |
|
|
6412 |
" <td>0.000000</td>\n", |
|
|
6413 |
" <td>0.000000</td>\n", |
|
|
6414 |
" <td>...</td>\n", |
|
|
6415 |
" <td>0.000000</td>\n", |
|
|
6416 |
" <td>-1.043943</td>\n", |
|
|
6417 |
" <td>-0.524915</td>\n", |
|
|
6418 |
" <td>0.000000</td>\n", |
|
|
6419 |
" <td>0.000000</td>\n", |
|
|
6420 |
" <td>0.000000</td>\n", |
|
|
6421 |
" <td>-0.377070</td>\n", |
|
|
6422 |
" <td>-0.643856</td>\n", |
|
|
6423 |
" <td>0.000000</td>\n", |
|
|
6424 |
" <td>0.000000</td>\n", |
|
|
6425 |
" </tr>\n", |
|
|
6426 |
" <tr>\n", |
|
|
6427 |
" <th>119016</th>\n", |
|
|
6428 |
" <td>0.448901</td>\n", |
|
|
6429 |
" <td>-0.286304</td>\n", |
|
|
6430 |
" <td>0.000000</td>\n", |
|
|
6431 |
" <td>0.000000</td>\n", |
|
|
6432 |
" <td>0.000000</td>\n", |
|
|
6433 |
" <td>-0.242977</td>\n", |
|
|
6434 |
" <td>0.000000</td>\n", |
|
|
6435 |
" <td>-0.286304</td>\n", |
|
|
6436 |
" <td>0.000000</td>\n", |
|
|
6437 |
" <td>0.000000</td>\n", |
|
|
6438 |
" <td>...</td>\n", |
|
|
6439 |
" <td>0.000000</td>\n", |
|
|
6440 |
" <td>-1.014500</td>\n", |
|
|
6441 |
" <td>-0.473931</td>\n", |
|
|
6442 |
" <td>0.000000</td>\n", |
|
|
6443 |
" <td>0.000000</td>\n", |
|
|
6444 |
" <td>0.000000</td>\n", |
|
|
6445 |
" <td>-0.367732</td>\n", |
|
|
6446 |
" <td>-0.577767</td>\n", |
|
|
6447 |
" <td>0.000000</td>\n", |
|
|
6448 |
" <td>0.000000</td>\n", |
|
|
6449 |
" </tr>\n", |
|
|
6450 |
" <tr>\n", |
|
|
6451 |
" <th>84458</th>\n", |
|
|
6452 |
" <td>0.389567</td>\n", |
|
|
6453 |
" <td>-0.666576</td>\n", |
|
|
6454 |
" <td>0.000000</td>\n", |
|
|
6455 |
" <td>0.000000</td>\n", |
|
|
6456 |
" <td>0.000000</td>\n", |
|
|
6457 |
" <td>-0.340075</td>\n", |
|
|
6458 |
" <td>0.000000</td>\n", |
|
|
6459 |
" <td>-0.367732</td>\n", |
|
|
6460 |
" <td>0.000000</td>\n", |
|
|
6461 |
" <td>0.000000</td>\n", |
|
|
6462 |
" <td>...</td>\n", |
|
|
6463 |
" <td>0.000000</td>\n", |
|
|
6464 |
" <td>-1.014500</td>\n", |
|
|
6465 |
" <td>-0.473931</td>\n", |
|
|
6466 |
" <td>0.000000</td>\n", |
|
|
6467 |
" <td>0.000000</td>\n", |
|
|
6468 |
" <td>0.000000</td>\n", |
|
|
6469 |
" <td>-0.386468</td>\n", |
|
|
6470 |
" <td>-0.610433</td>\n", |
|
|
6471 |
" <td>-0.577767</td>\n", |
|
|
6472 |
" <td>0.000000</td>\n", |
|
|
6473 |
" </tr>\n", |
|
|
6474 |
" <tr>\n", |
|
|
6475 |
" <th>84458</th>\n", |
|
|
6476 |
" <td>0.389567</td>\n", |
|
|
6477 |
" <td>-0.666576</td>\n", |
|
|
6478 |
" <td>0.000000</td>\n", |
|
|
6479 |
" <td>0.000000</td>\n", |
|
|
6480 |
" <td>0.000000</td>\n", |
|
|
6481 |
" <td>-0.340075</td>\n", |
|
|
6482 |
" <td>0.000000</td>\n", |
|
|
6483 |
" <td>-0.367732</td>\n", |
|
|
6484 |
" <td>0.000000</td>\n", |
|
|
6485 |
" <td>0.000000</td>\n", |
|
|
6486 |
" <td>...</td>\n", |
|
|
6487 |
" <td>0.000000</td>\n", |
|
|
6488 |
" <td>-1.014500</td>\n", |
|
|
6489 |
" <td>-0.473931</td>\n", |
|
|
6490 |
" <td>0.000000</td>\n", |
|
|
6491 |
" <td>0.000000</td>\n", |
|
|
6492 |
" <td>0.000000</td>\n", |
|
|
6493 |
" <td>-0.386468</td>\n", |
|
|
6494 |
" <td>-0.610433</td>\n", |
|
|
6495 |
" <td>-0.577767</td>\n", |
|
|
6496 |
" <td>0.000000</td>\n", |
|
|
6497 |
" </tr>\n", |
|
|
6498 |
" <tr>\n", |
|
|
6499 |
" <th>574445</th>\n", |
|
|
6500 |
" <td>0.490570</td>\n", |
|
|
6501 |
" <td>0.000000</td>\n", |
|
|
6502 |
" <td>-0.286304</td>\n", |
|
|
6503 |
" <td>0.000000</td>\n", |
|
|
6504 |
" <td>0.000000</td>\n", |
|
|
6505 |
" <td>-1.074001</td>\n", |
|
|
6506 |
" <td>0.000000</td>\n", |
|
|
6507 |
" <td>0.238787</td>\n", |
|
|
6508 |
" <td>0.000000</td>\n", |
|
|
6509 |
" <td>0.000000</td>\n", |
|
|
6510 |
" <td>...</td>\n", |
|
|
6511 |
" <td>-0.823677</td>\n", |
|
|
6512 |
" <td>-0.957356</td>\n", |
|
|
6513 |
" <td>-0.321928</td>\n", |
|
|
6514 |
" <td>0.000000</td>\n", |
|
|
6515 |
" <td>-0.985645</td>\n", |
|
|
6516 |
" <td>-0.454032</td>\n", |
|
|
6517 |
" <td>0.000000</td>\n", |
|
|
6518 |
" <td>-0.599462</td>\n", |
|
|
6519 |
" <td>-0.577767</td>\n", |
|
|
6520 |
" <td>0.000000</td>\n", |
|
|
6521 |
" </tr>\n", |
|
|
6522 |
" <tr>\n", |
|
|
6523 |
" <th>574445</th>\n", |
|
|
6524 |
" <td>0.490570</td>\n", |
|
|
6525 |
" <td>0.000000</td>\n", |
|
|
6526 |
" <td>-0.286304</td>\n", |
|
|
6527 |
" <td>0.000000</td>\n", |
|
|
6528 |
" <td>0.000000</td>\n", |
|
|
6529 |
" <td>-1.074001</td>\n", |
|
|
6530 |
" <td>0.000000</td>\n", |
|
|
6531 |
" <td>0.238787</td>\n", |
|
|
6532 |
" <td>0.000000</td>\n", |
|
|
6533 |
" <td>0.000000</td>\n", |
|
|
6534 |
" <td>...</td>\n", |
|
|
6535 |
" <td>-0.823677</td>\n", |
|
|
6536 |
" <td>-0.957356</td>\n", |
|
|
6537 |
" <td>-0.321928</td>\n", |
|
|
6538 |
" <td>0.000000</td>\n", |
|
|
6539 |
" <td>-0.985645</td>\n", |
|
|
6540 |
" <td>-0.454032</td>\n", |
|
|
6541 |
" <td>0.000000</td>\n", |
|
|
6542 |
" <td>-0.599462</td>\n", |
|
|
6543 |
" <td>-0.577767</td>\n", |
|
|
6544 |
" <td>0.000000</td>\n", |
|
|
6545 |
" </tr>\n", |
|
|
6546 |
" <tr>\n", |
|
|
6547 |
" <th>26095</th>\n", |
|
|
6548 |
" <td>0.531069</td>\n", |
|
|
6549 |
" <td>0.000000</td>\n", |
|
|
6550 |
" <td>0.000000</td>\n", |
|
|
6551 |
" <td>0.000000</td>\n", |
|
|
6552 |
" <td>0.000000</td>\n", |
|
|
6553 |
" <td>-0.251539</td>\n", |
|
|
6554 |
" <td>0.000000</td>\n", |
|
|
6555 |
" <td>-0.286304</td>\n", |
|
|
6556 |
" <td>0.000000</td>\n", |
|
|
6557 |
" <td>0.790772</td>\n", |
|
|
6558 |
" <td>...</td>\n", |
|
|
6559 |
" <td>0.269033</td>\n", |
|
|
6560 |
" <td>-1.043943</td>\n", |
|
|
6561 |
" <td>0.000000</td>\n", |
|
|
6562 |
" <td>0.000000</td>\n", |
|
|
6563 |
" <td>0.000000</td>\n", |
|
|
6564 |
" <td>0.000000</td>\n", |
|
|
6565 |
" <td>0.000000</td>\n", |
|
|
6566 |
" <td>-0.588574</td>\n", |
|
|
6567 |
" <td>0.000000</td>\n", |
|
|
6568 |
" <td>0.000000</td>\n", |
|
|
6569 |
" </tr>\n", |
|
|
6570 |
" <tr>\n", |
|
|
6571 |
" <th>26095</th>\n", |
|
|
6572 |
" <td>0.531069</td>\n", |
|
|
6573 |
" <td>0.000000</td>\n", |
|
|
6574 |
" <td>0.000000</td>\n", |
|
|
6575 |
" <td>0.000000</td>\n", |
|
|
6576 |
" <td>0.000000</td>\n", |
|
|
6577 |
" <td>-0.251539</td>\n", |
|
|
6578 |
" <td>0.000000</td>\n", |
|
|
6579 |
" <td>-0.286304</td>\n", |
|
|
6580 |
" <td>0.000000</td>\n", |
|
|
6581 |
" <td>0.790772</td>\n", |
|
|
6582 |
" <td>...</td>\n", |
|
|
6583 |
" <td>0.269033</td>\n", |
|
|
6584 |
" <td>-1.043943</td>\n", |
|
|
6585 |
" <td>0.000000</td>\n", |
|
|
6586 |
" <td>0.000000</td>\n", |
|
|
6587 |
" <td>0.000000</td>\n", |
|
|
6588 |
" <td>0.000000</td>\n", |
|
|
6589 |
" <td>0.000000</td>\n", |
|
|
6590 |
" <td>-0.588574</td>\n", |
|
|
6591 |
" <td>0.000000</td>\n", |
|
|
6592 |
" <td>0.000000</td>\n", |
|
|
6593 |
" </tr>\n", |
|
|
6594 |
" <tr>\n", |
|
|
6595 |
" <th>84968</th>\n", |
|
|
6596 |
" <td>-0.736966</td>\n", |
|
|
6597 |
" <td>-0.321928</td>\n", |
|
|
6598 |
" <td>0.000000</td>\n", |
|
|
6599 |
" <td>0.570463</td>\n", |
|
|
6600 |
" <td>0.000000</td>\n", |
|
|
6601 |
" <td>0.000000</td>\n", |
|
|
6602 |
" <td>0.000000</td>\n", |
|
|
6603 |
" <td>-0.875672</td>\n", |
|
|
6604 |
" <td>-0.678072</td>\n", |
|
|
6605 |
" <td>0.378512</td>\n", |
|
|
6606 |
" <td>...</td>\n", |
|
|
6607 |
" <td>0.000000</td>\n", |
|
|
6608 |
" <td>-1.000000</td>\n", |
|
|
6609 |
" <td>0.250962</td>\n", |
|
|
6610 |
" <td>0.000000</td>\n", |
|
|
6611 |
" <td>0.000000</td>\n", |
|
|
6612 |
" <td>0.000000</td>\n", |
|
|
6613 |
" <td>0.000000</td>\n", |
|
|
6614 |
" <td>-0.545824</td>\n", |
|
|
6615 |
" <td>-0.545824</td>\n", |
|
|
6616 |
" <td>-0.535332</td>\n", |
|
|
6617 |
" </tr>\n", |
|
|
6618 |
" <tr>\n", |
|
|
6619 |
" <th>84968</th>\n", |
|
|
6620 |
" <td>-0.736966</td>\n", |
|
|
6621 |
" <td>-0.321928</td>\n", |
|
|
6622 |
" <td>0.000000</td>\n", |
|
|
6623 |
" <td>0.570463</td>\n", |
|
|
6624 |
" <td>0.000000</td>\n", |
|
|
6625 |
" <td>0.000000</td>\n", |
|
|
6626 |
" <td>0.000000</td>\n", |
|
|
6627 |
" <td>-0.875672</td>\n", |
|
|
6628 |
" <td>-0.678072</td>\n", |
|
|
6629 |
" <td>0.378512</td>\n", |
|
|
6630 |
" <td>...</td>\n", |
|
|
6631 |
" <td>0.000000</td>\n", |
|
|
6632 |
" <td>-1.000000</td>\n", |
|
|
6633 |
" <td>0.250962</td>\n", |
|
|
6634 |
" <td>0.000000</td>\n", |
|
|
6635 |
" <td>0.000000</td>\n", |
|
|
6636 |
" <td>0.000000</td>\n", |
|
|
6637 |
" <td>0.000000</td>\n", |
|
|
6638 |
" <td>-0.545824</td>\n", |
|
|
6639 |
" <td>-0.545824</td>\n", |
|
|
6640 |
" <td>-0.535332</td>\n", |
|
|
6641 |
" </tr>\n", |
|
|
6642 |
" <tr>\n", |
|
|
6643 |
" <th>80759</th>\n", |
|
|
6644 |
" <td>-0.556393</td>\n", |
|
|
6645 |
" <td>0.599318</td>\n", |
|
|
6646 |
" <td>0.000000</td>\n", |
|
|
6647 |
" <td>0.000000</td>\n", |
|
|
6648 |
" <td>0.000000</td>\n", |
|
|
6649 |
" <td>0.250962</td>\n", |
|
|
6650 |
" <td>0.000000</td>\n", |
|
|
6651 |
" <td>-0.386468</td>\n", |
|
|
6652 |
" <td>-0.567041</td>\n", |
|
|
6653 |
" <td>-0.556393</td>\n", |
|
|
6654 |
" <td>...</td>\n", |
|
|
6655 |
" <td>0.000000</td>\n", |
|
|
6656 |
" <td>0.000000</td>\n", |
|
|
6657 |
" <td>-0.621488</td>\n", |
|
|
6658 |
" <td>-0.454032</td>\n", |
|
|
6659 |
" <td>0.000000</td>\n", |
|
|
6660 |
" <td>0.000000</td>\n", |
|
|
6661 |
" <td>-0.386468</td>\n", |
|
|
6662 |
" <td>-0.621488</td>\n", |
|
|
6663 |
" <td>0.761285</td>\n", |
|
|
6664 |
" <td>0.000000</td>\n", |
|
|
6665 |
" </tr>\n", |
|
|
6666 |
" <tr>\n", |
|
|
6667 |
" <th>80759</th>\n", |
|
|
6668 |
" <td>-0.556393</td>\n", |
|
|
6669 |
" <td>0.599318</td>\n", |
|
|
6670 |
" <td>0.000000</td>\n", |
|
|
6671 |
" <td>0.000000</td>\n", |
|
|
6672 |
" <td>0.000000</td>\n", |
|
|
6673 |
" <td>0.250962</td>\n", |
|
|
6674 |
" <td>0.000000</td>\n", |
|
|
6675 |
" <td>-0.386468</td>\n", |
|
|
6676 |
" <td>-0.567041</td>\n", |
|
|
6677 |
" <td>-0.556393</td>\n", |
|
|
6678 |
" <td>...</td>\n", |
|
|
6679 |
" <td>0.000000</td>\n", |
|
|
6680 |
" <td>0.000000</td>\n", |
|
|
6681 |
" <td>-0.621488</td>\n", |
|
|
6682 |
" <td>-0.454032</td>\n", |
|
|
6683 |
" <td>0.000000</td>\n", |
|
|
6684 |
" <td>0.000000</td>\n", |
|
|
6685 |
" <td>-0.386468</td>\n", |
|
|
6686 |
" <td>-0.621488</td>\n", |
|
|
6687 |
" <td>0.761285</td>\n", |
|
|
6688 |
" <td>0.000000</td>\n", |
|
|
6689 |
" </tr>\n", |
|
|
6690 |
" <tr>\n", |
|
|
6691 |
" <th>3192</th>\n", |
|
|
6692 |
" <td>1.350497</td>\n", |
|
|
6693 |
" <td>0.632268</td>\n", |
|
|
6694 |
" <td>0.000000</td>\n", |
|
|
6695 |
" <td>0.000000</td>\n", |
|
|
6696 |
" <td>0.000000</td>\n", |
|
|
6697 |
" <td>0.220330</td>\n", |
|
|
6698 |
" <td>0.000000</td>\n", |
|
|
6699 |
" <td>0.448901</td>\n", |
|
|
6700 |
" <td>-0.268817</td>\n", |
|
|
6701 |
" <td>0.000000</td>\n", |
|
|
6702 |
" <td>...</td>\n", |
|
|
6703 |
" <td>0.480265</td>\n", |
|
|
6704 |
" <td>0.000000</td>\n", |
|
|
6705 |
" <td>0.207893</td>\n", |
|
|
6706 |
" <td>0.000000</td>\n", |
|
|
6707 |
" <td>0.000000</td>\n", |
|
|
6708 |
" <td>-0.330973</td>\n", |
|
|
6709 |
" <td>0.250962</td>\n", |
|
|
6710 |
" <td>0.000000</td>\n", |
|
|
6711 |
" <td>1.021480</td>\n", |
|
|
6712 |
" <td>0.599318</td>\n", |
|
|
6713 |
" </tr>\n", |
|
|
6714 |
" <tr>\n", |
|
|
6715 |
" <th>3192</th>\n", |
|
|
6716 |
" <td>1.350497</td>\n", |
|
|
6717 |
" <td>0.632268</td>\n", |
|
|
6718 |
" <td>0.000000</td>\n", |
|
|
6719 |
" <td>0.000000</td>\n", |
|
|
6720 |
" <td>0.000000</td>\n", |
|
|
6721 |
" <td>0.220330</td>\n", |
|
|
6722 |
" <td>0.000000</td>\n", |
|
|
6723 |
" <td>0.448901</td>\n", |
|
|
6724 |
" <td>-0.268817</td>\n", |
|
|
6725 |
" <td>0.000000</td>\n", |
|
|
6726 |
" <td>...</td>\n", |
|
|
6727 |
" <td>0.480265</td>\n", |
|
|
6728 |
" <td>0.000000</td>\n", |
|
|
6729 |
" <td>0.207893</td>\n", |
|
|
6730 |
" <td>0.000000</td>\n", |
|
|
6731 |
" <td>0.000000</td>\n", |
|
|
6732 |
" <td>-0.330973</td>\n", |
|
|
6733 |
" <td>0.250962</td>\n", |
|
|
6734 |
" <td>0.000000</td>\n", |
|
|
6735 |
" <td>1.021480</td>\n", |
|
|
6736 |
" <td>0.599318</td>\n", |
|
|
6737 |
" </tr>\n", |
|
|
6738 |
" <tr>\n", |
|
|
6739 |
" <th>387707</th>\n", |
|
|
6740 |
" <td>0.389567</td>\n", |
|
|
6741 |
" <td>-0.666576</td>\n", |
|
|
6742 |
" <td>0.000000</td>\n", |
|
|
6743 |
" <td>0.000000</td>\n", |
|
|
6744 |
" <td>0.000000</td>\n", |
|
|
6745 |
" <td>-0.340075</td>\n", |
|
|
6746 |
" <td>0.000000</td>\n", |
|
|
6747 |
" <td>-0.367732</td>\n", |
|
|
6748 |
" <td>0.000000</td>\n", |
|
|
6749 |
" <td>0.000000</td>\n", |
|
|
6750 |
" <td>...</td>\n", |
|
|
6751 |
" <td>0.000000</td>\n", |
|
|
6752 |
" <td>-1.014500</td>\n", |
|
|
6753 |
" <td>-0.473931</td>\n", |
|
|
6754 |
" <td>0.000000</td>\n", |
|
|
6755 |
" <td>0.000000</td>\n", |
|
|
6756 |
" <td>0.000000</td>\n", |
|
|
6757 |
" <td>-0.386468</td>\n", |
|
|
6758 |
" <td>-0.610433</td>\n", |
|
|
6759 |
" <td>-0.577767</td>\n", |
|
|
6760 |
" <td>0.000000</td>\n", |
|
|
6761 |
" </tr>\n", |
|
|
6762 |
" <tr>\n", |
|
|
6763 |
" <th>387707</th>\n", |
|
|
6764 |
" <td>0.389567</td>\n", |
|
|
6765 |
" <td>-0.666576</td>\n", |
|
|
6766 |
" <td>0.000000</td>\n", |
|
|
6767 |
" <td>0.000000</td>\n", |
|
|
6768 |
" <td>0.000000</td>\n", |
|
|
6769 |
" <td>-0.340075</td>\n", |
|
|
6770 |
" <td>0.000000</td>\n", |
|
|
6771 |
" <td>-0.367732</td>\n", |
|
|
6772 |
" <td>0.000000</td>\n", |
|
|
6773 |
" <td>0.000000</td>\n", |
|
|
6774 |
" <td>...</td>\n", |
|
|
6775 |
" <td>0.000000</td>\n", |
|
|
6776 |
" <td>-1.014500</td>\n", |
|
|
6777 |
" <td>-0.473931</td>\n", |
|
|
6778 |
" <td>0.000000</td>\n", |
|
|
6779 |
" <td>0.000000</td>\n", |
|
|
6780 |
" <td>0.000000</td>\n", |
|
|
6781 |
" <td>-0.386468</td>\n", |
|
|
6782 |
" <td>-0.610433</td>\n", |
|
|
6783 |
" <td>-0.577767</td>\n", |
|
|
6784 |
" <td>0.000000</td>\n", |
|
|
6785 |
" </tr>\n", |
|
|
6786 |
" <tr>\n", |
|
|
6787 |
" <th>79741</th>\n", |
|
|
6788 |
" <td>0.000000</td>\n", |
|
|
6789 |
" <td>0.589763</td>\n", |
|
|
6790 |
" <td>0.000000</td>\n", |
|
|
6791 |
" <td>0.000000</td>\n", |
|
|
6792 |
" <td>0.000000</td>\n", |
|
|
6793 |
" <td>-0.242977</td>\n", |
|
|
6794 |
" <td>0.000000</td>\n", |
|
|
6795 |
" <td>0.207893</td>\n", |
|
|
6796 |
" <td>0.000000</td>\n", |
|
|
6797 |
" <td>0.000000</td>\n", |
|
|
6798 |
" <td>...</td>\n", |
|
|
6799 |
" <td>-0.798366</td>\n", |
|
|
6800 |
" <td>-0.985645</td>\n", |
|
|
6801 |
" <td>-0.358454</td>\n", |
|
|
6802 |
" <td>0.000000</td>\n", |
|
|
6803 |
" <td>0.700440</td>\n", |
|
|
6804 |
" <td>0.000000</td>\n", |
|
|
6805 |
" <td>-0.367732</td>\n", |
|
|
6806 |
" <td>-0.588574</td>\n", |
|
|
6807 |
" <td>0.459432</td>\n", |
|
|
6808 |
" <td>0.000000</td>\n", |
|
|
6809 |
" </tr>\n", |
|
|
6810 |
" <tr>\n", |
|
|
6811 |
" <th>79741</th>\n", |
|
|
6812 |
" <td>0.000000</td>\n", |
|
|
6813 |
" <td>0.589763</td>\n", |
|
|
6814 |
" <td>0.000000</td>\n", |
|
|
6815 |
" <td>0.000000</td>\n", |
|
|
6816 |
" <td>0.000000</td>\n", |
|
|
6817 |
" <td>-0.242977</td>\n", |
|
|
6818 |
" <td>0.000000</td>\n", |
|
|
6819 |
" <td>0.207893</td>\n", |
|
|
6820 |
" <td>0.000000</td>\n", |
|
|
6821 |
" <td>0.220330</td>\n", |
|
|
6822 |
" <td>...</td>\n", |
|
|
6823 |
" <td>-0.798366</td>\n", |
|
|
6824 |
" <td>-0.985645</td>\n", |
|
|
6825 |
" <td>0.000000</td>\n", |
|
|
6826 |
" <td>0.000000</td>\n", |
|
|
6827 |
" <td>0.700440</td>\n", |
|
|
6828 |
" <td>0.000000</td>\n", |
|
|
6829 |
" <td>-0.367732</td>\n", |
|
|
6830 |
" <td>-0.588574</td>\n", |
|
|
6831 |
" <td>0.459432</td>\n", |
|
|
6832 |
" <td>0.269033</td>\n", |
|
|
6833 |
" </tr>\n", |
|
|
6834 |
" </tbody>\n", |
|
|
6835 |
"</table>\n", |
|
|
6836 |
"<p>77 rows × 375 columns</p>\n", |
|
|
6837 |
"</div>" |
|
|
6838 |
], |
|
|
6839 |
"text/plain": [ |
|
|
6840 |
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 \\\n", |
|
|
6841 |
"gene_id \n", |
|
|
6842 |
"143872 0.000000 0.560715 0.000000 0.000000 0.000000 -0.330973 \n", |
|
|
6843 |
"143872 0.000000 0.560715 0.000000 0.000000 0.000000 -0.330973 \n", |
|
|
6844 |
"286464 0.000000 0.378512 0.000000 0.550901 0.000000 -0.524915 \n", |
|
|
6845 |
"286464 0.000000 0.378512 0.000000 0.550901 0.000000 -0.524915 \n", |
|
|
6846 |
"286464 0.000000 0.378512 0.000000 0.550901 0.000000 -0.524915 \n", |
|
|
6847 |
"51463 1.238787 1.090853 0.000000 0.000000 0.000000 1.839960 \n", |
|
|
6848 |
"51463 1.238787 1.090853 0.000000 0.000000 0.000000 1.839960 \n", |
|
|
6849 |
"642826 0.608809 0.859970 0.531069 0.000000 0.000000 0.871844 \n", |
|
|
6850 |
"642826 0.608809 0.859970 0.531069 0.000000 0.000000 0.871844 \n", |
|
|
6851 |
"653067 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
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6852 |
"653067 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
|
|
6853 |
"653067 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
|
|
6854 |
"653067 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
|
|
6855 |
"399761 0.531069 0.718088 0.000000 0.000000 0.000000 -0.251539 \n", |
|
|
6856 |
"399761 0.531069 0.718088 0.000000 0.000000 0.000000 -0.251539 \n", |
|
|
6857 |
"647060 0.000000 0.000000 0.000000 0.000000 0.000000 -0.312939 \n", |
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6858 |
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|
6859 |
"284565 1.238787 1.090853 0.000000 0.000000 0.000000 1.570463 \n", |
|
|
6860 |
"284565 1.238787 1.090853 0.000000 0.000000 0.000000 1.310340 \n", |
|
|
6861 |
"84631 -0.823677 -0.524915 0.000000 0.632268 0.000000 -1.074001 \n", |
|
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6862 |
"84631 -0.823677 -0.524915 0.000000 0.632268 0.000000 -1.074001 \n", |
|
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6863 |
"161176 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", |
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6864 |
"161176 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
6865 |
"341019 0.959770 0.000000 0.000000 0.000000 0.000000 -0.304006 \n", |
|
|
6866 |
"341019 0.959770 0.000000 0.000000 0.000000 0.000000 -0.304006 \n", |
|
|
6867 |
"83869 -3.000000 -3.184425 -3.321928 -3.000000 -2.599462 -3.556393 \n", |
|
|
6868 |
"83869 -3.000000 -3.184425 -3.321928 -3.000000 -2.599462 -3.556393 \n", |
|
|
6869 |
"9502 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
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6870 |
"9502 0.000000 0.378512 0.000000 0.550901 0.000000 -0.434403 \n", |
|
|
6871 |
"83871 0.000000 0.000000 0.000000 0.500802 0.000000 -0.304006 \n", |
|
|
6872 |
"... ... ... ... ... ... ... \n", |
|
|
6873 |
"100134869 0.000000 0.207893 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
6874 |
"100134869 0.000000 0.207893 0.000000 0.000000 0.000000 0.000000 \n", |
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|
6875 |
"84316 -0.251539 0.000000 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6876 |
"84316 -0.810966 -0.689660 0.000000 0.000000 0.000000 0.718088 \n", |
|
|
6877 |
"200030 1.238787 1.090853 0.000000 0.000000 0.000000 1.839960 \n", |
|
|
6878 |
"200030 1.238787 1.090853 0.000000 0.000000 0.000000 1.839960 \n", |
|
|
6879 |
"642658 1.049631 1.358959 0.000000 0.599318 0.000000 0.000000 \n", |
|
|
6880 |
"642658 1.049631 1.358959 0.000000 0.599318 0.000000 0.000000 \n", |
|
|
6881 |
"100302179 0.778209 0.000000 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6882 |
"100302179 0.778209 0.000000 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6883 |
"401508 0.232661 0.000000 0.000000 0.000000 0.250962 0.000000 \n", |
|
|
6884 |
"401508 0.232661 0.000000 0.000000 0.000000 0.250962 0.000000 \n", |
|
|
6885 |
"119016 0.378512 0.570463 0.000000 0.000000 0.000000 -0.251539 \n", |
|
|
6886 |
"119016 0.448901 -0.286304 0.000000 0.000000 0.000000 -0.242977 \n", |
|
|
6887 |
"84458 0.389567 -0.666576 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6888 |
"84458 0.389567 -0.666576 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6889 |
"574445 0.490570 0.000000 -0.286304 0.000000 0.000000 -1.074001 \n", |
|
|
6890 |
"574445 0.490570 0.000000 -0.286304 0.000000 0.000000 -1.074001 \n", |
|
|
6891 |
"26095 0.531069 0.000000 0.000000 0.000000 0.000000 -0.251539 \n", |
|
|
6892 |
"26095 0.531069 0.000000 0.000000 0.000000 0.000000 -0.251539 \n", |
|
|
6893 |
"84968 -0.736966 -0.321928 0.000000 0.570463 0.000000 0.000000 \n", |
|
|
6894 |
"84968 -0.736966 -0.321928 0.000000 0.570463 0.000000 0.000000 \n", |
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|
6895 |
"80759 -0.556393 0.599318 0.000000 0.000000 0.000000 0.250962 \n", |
|
|
6896 |
"80759 -0.556393 0.599318 0.000000 0.000000 0.000000 0.250962 \n", |
|
|
6897 |
"3192 1.350497 0.632268 0.000000 0.000000 0.000000 0.220330 \n", |
|
|
6898 |
"3192 1.350497 0.632268 0.000000 0.000000 0.000000 0.220330 \n", |
|
|
6899 |
"387707 0.389567 -0.666576 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6900 |
"387707 0.389567 -0.666576 0.000000 0.000000 0.000000 -0.340075 \n", |
|
|
6901 |
"79741 0.000000 0.589763 0.000000 0.000000 0.000000 -0.242977 \n", |
|
|
6902 |
"79741 0.000000 0.589763 0.000000 0.000000 0.000000 -0.242977 \n", |
|
|
6903 |
"\n", |
|
|
6904 |
" X-1167 X-1169 X-1172 X-1173 ... X-5694 \\\n", |
|
|
6905 |
"gene_id ... \n", |
|
|
6906 |
"143872 0.000000 -0.367732 0.350497 0.000000 ... 0.000000 \n", |
|
|
6907 |
"143872 0.000000 -0.367732 0.350497 0.000000 ... 0.000000 \n", |
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6908 |
"286464 0.000000 -0.902389 -1.321928 0.367371 ... 0.000000 \n", |
|
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6909 |
"286464 0.000000 -0.902389 -1.321928 0.367371 ... 0.000000 \n", |
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6910 |
"286464 0.000000 -0.902389 -1.321928 0.367371 ... 0.000000 \n", |
|
|
6911 |
"51463 0.000000 0.448901 0.000000 0.000000 ... 0.469886 \n", |
|
|
6912 |
"51463 0.000000 0.448901 0.000000 0.000000 ... 0.438293 \n", |
|
|
6913 |
"642826 0.000000 -0.286304 0.000000 0.000000 ... 0.000000 \n", |
|
|
6914 |
"642826 0.000000 -0.286304 0.000000 0.000000 ... 0.000000 \n", |
|
|
6915 |
"653067 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6916 |
"653067 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6917 |
"653067 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6918 |
"653067 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6919 |
"399761 0.000000 -0.286304 0.000000 0.790772 ... 0.367371 \n", |
|
|
6920 |
"399761 0.000000 -0.286304 0.000000 0.790772 ... 0.367371 \n", |
|
|
6921 |
"647060 0.000000 -0.321928 0.000000 0.618239 ... 0.000000 \n", |
|
|
6922 |
"647060 0.000000 -0.321928 0.000000 0.618239 ... 0.000000 \n", |
|
|
6923 |
"284565 0.000000 0.448901 0.411426 0.448901 ... 0.469886 \n", |
|
|
6924 |
"284565 0.000000 0.448901 0.411426 0.448901 ... 0.469886 \n", |
|
|
6925 |
"84631 0.000000 -0.875672 -0.678072 0.378512 ... 0.000000 \n", |
|
|
6926 |
"84631 0.000000 -0.875672 -0.678072 0.378512 ... 0.000000 \n", |
|
|
6927 |
"161176 0.000000 -0.358454 0.250962 0.339137 ... -0.875672 \n", |
|
|
6928 |
"161176 0.000000 -0.358454 0.250962 0.339137 ... -0.875672 \n", |
|
|
6929 |
"341019 0.000000 -0.349235 0.000000 0.000000 ... 0.000000 \n", |
|
|
6930 |
"341019 0.000000 -0.349235 0.000000 0.000000 ... 0.000000 \n", |
|
|
6931 |
"83869 -2.785875 -0.875672 -2.736966 -2.514573 ... -2.556393 \n", |
|
|
6932 |
"83869 -2.785875 -0.875672 -2.736966 -2.514573 ... -2.556393 \n", |
|
|
6933 |
"9502 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6934 |
"9502 0.000000 -0.902389 1.220330 0.367371 ... 0.000000 \n", |
|
|
6935 |
"83871 0.000000 -0.349235 0.327687 0.000000 ... 0.000000 \n", |
|
|
6936 |
"... ... ... ... ... ... ... \n", |
|
|
6937 |
"100134869 0.000000 0.000000 0.232661 0.000000 ... 0.000000 \n", |
|
|
6938 |
"100134869 0.000000 0.000000 0.232661 0.000000 ... 0.000000 \n", |
|
|
6939 |
"84316 0.000000 -0.349235 -0.588574 0.000000 ... 0.000000 \n", |
|
|
6940 |
"84316 0.000000 0.000000 0.731183 0.367371 ... 0.000000 \n", |
|
|
6941 |
"200030 0.000000 0.448901 0.000000 0.000000 ... 0.438293 \n", |
|
|
6942 |
"200030 0.000000 0.448901 0.000000 0.000000 ... 0.438293 \n", |
|
|
6943 |
"642658 0.000000 0.321928 0.700440 0.298658 ... 0.632268 \n", |
|
|
6944 |
"642658 0.000000 0.321928 0.700440 0.298658 ... 0.632268 \n", |
|
|
6945 |
"100302179 0.000000 0.000000 0.000000 0.000000 ... 0.000000 \n", |
|
|
6946 |
"100302179 0.000000 0.000000 0.000000 0.000000 ... 0.000000 \n", |
|
|
6947 |
"401508 0.207893 0.000000 -0.666576 1.629939 ... 0.000000 \n", |
|
|
6948 |
"401508 0.207893 0.000000 -0.666576 1.629939 ... 0.000000 \n", |
|
|
6949 |
"119016 0.000000 -0.286304 0.000000 0.000000 ... 0.000000 \n", |
|
|
6950 |
"119016 0.000000 -0.286304 0.000000 0.000000 ... 0.000000 \n", |
|
|
6951 |
"84458 0.000000 -0.367732 0.000000 0.000000 ... 0.000000 \n", |
|
|
6952 |
"84458 0.000000 -0.367732 0.000000 0.000000 ... 0.000000 \n", |
|
|
6953 |
"574445 0.000000 0.238787 0.000000 0.000000 ... -0.823677 \n", |
|
|
6954 |
"574445 0.000000 0.238787 0.000000 0.000000 ... -0.823677 \n", |
|
|
6955 |
"26095 0.000000 -0.286304 0.000000 0.790772 ... 0.269033 \n", |
|
|
6956 |
"26095 0.000000 -0.286304 0.000000 0.790772 ... 0.269033 \n", |
|
|
6957 |
"84968 0.000000 -0.875672 -0.678072 0.378512 ... 0.000000 \n", |
|
|
6958 |
"84968 0.000000 -0.875672 -0.678072 0.378512 ... 0.000000 \n", |
|
|
6959 |
"80759 0.000000 -0.386468 -0.567041 -0.556393 ... 0.000000 \n", |
|
|
6960 |
"80759 0.000000 -0.386468 -0.567041 -0.556393 ... 0.000000 \n", |
|
|
6961 |
"3192 0.000000 0.448901 -0.268817 0.000000 ... 0.480265 \n", |
|
|
6962 |
"3192 0.000000 0.448901 -0.268817 0.000000 ... 0.480265 \n", |
|
|
6963 |
"387707 0.000000 -0.367732 0.000000 0.000000 ... 0.000000 \n", |
|
|
6964 |
"387707 0.000000 -0.367732 0.000000 0.000000 ... 0.000000 \n", |
|
|
6965 |
"79741 0.000000 0.207893 0.000000 0.000000 ... -0.798366 \n", |
|
|
6966 |
"79741 0.000000 0.207893 0.000000 0.220330 ... -0.798366 \n", |
|
|
6967 |
"\n", |
|
|
6968 |
" X-5696 X-5713 X-5717 X-5727 X-5739 X-5808 \\\n", |
|
|
6969 |
"gene_id \n", |
|
|
6970 |
"143872 -0.349235 0.000000 -0.321928 -1.014500 -0.588574 0.000000 \n", |
|
|
6971 |
"143872 -0.349235 0.000000 -0.321928 -1.014500 -0.588574 0.000000 \n", |
|
|
6972 |
"286464 -1.014500 0.718088 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6973 |
"286464 -1.014500 0.718088 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6974 |
"286464 -1.014500 0.718088 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6975 |
"51463 0.000000 0.618239 0.201634 0.000000 -0.260152 -0.349235 \n", |
|
|
6976 |
"51463 0.000000 0.618239 0.201634 0.000000 -0.260152 0.000000 \n", |
|
|
6977 |
"642826 -1.014500 -0.473931 0.000000 0.618239 0.000000 -0.386468 \n", |
|
|
6978 |
"642826 -1.014500 -0.473931 0.000000 0.618239 0.000000 -0.386468 \n", |
|
|
6979 |
"653067 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6980 |
"653067 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6981 |
"653067 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6982 |
"653067 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6983 |
"399761 -1.535332 0.000000 0.000000 0.000000 0.000000 -0.599462 \n", |
|
|
6984 |
"399761 -1.535332 0.000000 0.000000 0.000000 0.000000 -0.599462 \n", |
|
|
6985 |
"647060 -0.621488 0.000000 -0.377070 -0.749038 -0.405451 0.000000 \n", |
|
|
6986 |
"647060 -0.621488 0.000000 -0.377070 -0.749038 -0.405451 0.000000 \n", |
|
|
6987 |
"284565 -0.504305 0.618239 0.201634 0.000000 -0.260152 0.000000 \n", |
|
|
6988 |
"284565 -0.524915 0.618239 0.201634 0.000000 -0.260152 0.000000 \n", |
|
|
6989 |
"84631 -1.014500 0.500802 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
6990 |
"84631 -1.014500 0.500802 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
6991 |
"161176 0.000000 -0.483985 0.000000 0.000000 -0.610433 0.000000 \n", |
|
|
6992 |
"161176 0.000000 -0.483985 0.000000 0.000000 -0.610433 0.000000 \n", |
|
|
6993 |
"341019 -0.666576 0.000000 -0.304006 -1.000000 -0.610433 0.000000 \n", |
|
|
6994 |
"341019 -0.312939 0.000000 -0.304006 -1.000000 -0.610433 0.000000 \n", |
|
|
6995 |
"83869 -3.943416 -2.785875 -2.152003 -3.556393 -3.251539 -2.736966 \n", |
|
|
6996 |
"83869 -3.943416 -2.785875 -2.152003 -3.556393 -3.251539 -2.736966 \n", |
|
|
6997 |
"9502 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6998 |
"9502 -1.014500 0.580145 0.000000 -1.014500 0.000000 0.000000 \n", |
|
|
6999 |
"83871 0.000000 -0.463947 -0.358454 0.000000 0.000000 0.000000 \n", |
|
|
7000 |
"... ... ... ... ... ... ... \n", |
|
|
7001 |
"100134869 0.389567 0.000000 0.000000 -0.463947 0.000000 -0.367732 \n", |
|
|
7002 |
"100134869 0.389567 0.000000 0.000000 -0.463947 0.000000 -0.367732 \n", |
|
|
7003 |
"84316 -0.985645 -0.358454 -0.340075 -0.971431 -0.545824 0.310340 \n", |
|
|
7004 |
"84316 0.000000 0.000000 -0.434403 1.060047 0.490570 0.000000 \n", |
|
|
7005 |
"200030 0.000000 0.618239 0.201634 0.000000 -0.260152 0.000000 \n", |
|
|
7006 |
"200030 0.000000 0.618239 0.201634 0.000000 -0.260152 0.000000 \n", |
|
|
7007 |
"642658 0.000000 0.769772 0.232661 1.121015 0.831877 -0.367732 \n", |
|
|
7008 |
"642658 0.000000 0.769772 0.232661 1.121015 0.831877 -0.367732 \n", |
|
|
7009 |
"100302179 0.000000 0.201634 -0.251539 0.000000 -0.463947 0.000000 \n", |
|
|
7010 |
"100302179 0.000000 0.201634 -0.251539 0.000000 -0.463947 0.000000 \n", |
|
|
7011 |
"401508 -2.321928 0.000000 0.000000 -0.260152 0.000000 -0.545824 \n", |
|
|
7012 |
"401508 -2.321928 0.000000 0.000000 -0.260152 0.000000 -0.545824 \n", |
|
|
7013 |
"119016 -1.043943 -0.524915 0.000000 0.000000 0.000000 -0.377070 \n", |
|
|
7014 |
"119016 -1.014500 -0.473931 0.000000 0.000000 0.000000 -0.367732 \n", |
|
|
7015 |
"84458 -1.014500 -0.473931 0.000000 0.000000 0.000000 -0.386468 \n", |
|
|
7016 |
"84458 -1.014500 -0.473931 0.000000 0.000000 0.000000 -0.386468 \n", |
|
|
7017 |
"574445 -0.957356 -0.321928 0.000000 -0.985645 -0.454032 0.000000 \n", |
|
|
7018 |
"574445 -0.957356 -0.321928 0.000000 -0.985645 -0.454032 0.000000 \n", |
|
|
7019 |
"26095 -1.043943 0.000000 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
7020 |
"26095 -1.043943 0.000000 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
7021 |
"84968 -1.000000 0.250962 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
7022 |
"84968 -1.000000 0.250962 0.000000 0.000000 0.000000 0.000000 \n", |
|
|
7023 |
"80759 0.000000 -0.621488 -0.454032 0.000000 0.000000 -0.386468 \n", |
|
|
7024 |
"80759 0.000000 -0.621488 -0.454032 0.000000 0.000000 -0.386468 \n", |
|
|
7025 |
"3192 0.000000 0.207893 0.000000 0.000000 -0.330973 0.250962 \n", |
|
|
7026 |
"3192 0.000000 0.207893 0.000000 0.000000 -0.330973 0.250962 \n", |
|
|
7027 |
"387707 -1.014500 -0.473931 0.000000 0.000000 0.000000 -0.386468 \n", |
|
|
7028 |
"387707 -1.014500 -0.473931 0.000000 0.000000 0.000000 -0.386468 \n", |
|
|
7029 |
"79741 -0.985645 -0.358454 0.000000 0.700440 0.000000 -0.367732 \n", |
|
|
7030 |
"79741 -0.985645 0.000000 0.000000 0.700440 0.000000 -0.367732 \n", |
|
|
7031 |
"\n", |
|
|
7032 |
" X-5959 X-5975 X-6047 \n", |
|
|
7033 |
"gene_id \n", |
|
|
7034 |
"143872 0.000000 0.000000 -0.514573 \n", |
|
|
7035 |
"143872 0.000000 0.000000 -0.514573 \n", |
|
|
7036 |
"286464 0.000000 -1.494109 -1.494109 \n", |
|
|
7037 |
"286464 0.000000 -1.494109 -1.494109 \n", |
|
|
7038 |
"286464 0.000000 -1.494109 -1.494109 \n", |
|
|
7039 |
"51463 0.000000 0.469886 0.000000 \n", |
|
|
7040 |
"51463 0.000000 0.469886 0.000000 \n", |
|
|
7041 |
"642826 -1.494109 -0.312939 0.000000 \n", |
|
|
7042 |
"642826 -1.494109 -0.312939 0.000000 \n", |
|
|
7043 |
"653067 -0.577767 -1.494109 -1.494109 \n", |
|
|
7044 |
"653067 -0.577767 -1.494109 -1.494109 \n", |
|
|
7045 |
"653067 -0.577767 -1.494109 -1.494109 \n", |
|
|
7046 |
"653067 -0.577767 -1.494109 -1.494109 \n", |
|
|
7047 |
"399761 -0.588574 0.000000 0.000000 \n", |
|
|
7048 |
"399761 -0.588574 0.000000 0.000000 \n", |
|
|
7049 |
"647060 -0.395929 0.000000 0.000000 \n", |
|
|
7050 |
"647060 -0.395929 0.000000 0.000000 \n", |
|
|
7051 |
"284565 0.000000 0.469886 0.000000 \n", |
|
|
7052 |
"284565 0.000000 0.469886 0.000000 \n", |
|
|
7053 |
"84631 -0.545824 -0.545824 -0.535332 \n", |
|
|
7054 |
"84631 -0.545824 -0.545824 -0.535332 \n", |
|
|
7055 |
"161176 0.411426 0.000000 0.000000 \n", |
|
|
7056 |
"161176 0.411426 0.000000 0.000000 \n", |
|
|
7057 |
"341019 0.000000 -0.444184 0.000000 \n", |
|
|
7058 |
"341019 0.000000 -0.444184 0.000000 \n", |
|
|
7059 |
"83869 -3.473931 -3.120294 -3.643856 \n", |
|
|
7060 |
"83869 -3.473931 -3.120294 -3.643856 \n", |
|
|
7061 |
"9502 -0.577767 -1.494109 -1.494109 \n", |
|
|
7062 |
"9502 -0.577767 -1.494109 -1.494109 \n", |
|
|
7063 |
"83871 0.448901 -0.535332 0.000000 \n", |
|
|
7064 |
"... ... ... ... \n", |
|
|
7065 |
"100134869 0.790772 0.000000 -0.535332 \n", |
|
|
7066 |
"100134869 0.790772 0.000000 -0.535332 \n", |
|
|
7067 |
"84316 0.438293 -0.473931 0.000000 \n", |
|
|
7068 |
"84316 -0.632629 -0.655172 0.000000 \n", |
|
|
7069 |
"200030 0.000000 0.469886 0.000000 \n", |
|
|
7070 |
"200030 0.000000 0.469886 0.000000 \n", |
|
|
7071 |
"642658 0.000000 1.121015 0.459432 \n", |
|
|
7072 |
"642658 0.000000 1.121015 0.459432 \n", |
|
|
7073 |
"100302179 0.000000 0.000000 0.000000 \n", |
|
|
7074 |
"100302179 0.000000 0.000000 0.000000 \n", |
|
|
7075 |
"401508 -0.330973 0.000000 0.000000 \n", |
|
|
7076 |
"401508 -0.330973 0.000000 0.000000 \n", |
|
|
7077 |
"119016 -0.643856 0.000000 0.000000 \n", |
|
|
7078 |
"119016 -0.577767 0.000000 0.000000 \n", |
|
|
7079 |
"84458 -0.610433 -0.577767 0.000000 \n", |
|
|
7080 |
"84458 -0.610433 -0.577767 0.000000 \n", |
|
|
7081 |
"574445 -0.599462 -0.577767 0.000000 \n", |
|
|
7082 |
"574445 -0.599462 -0.577767 0.000000 \n", |
|
|
7083 |
"26095 -0.588574 0.000000 0.000000 \n", |
|
|
7084 |
"26095 -0.588574 0.000000 0.000000 \n", |
|
|
7085 |
"84968 -0.545824 -0.545824 -0.535332 \n", |
|
|
7086 |
"84968 -0.545824 -0.545824 -0.535332 \n", |
|
|
7087 |
"80759 -0.621488 0.761285 0.000000 \n", |
|
|
7088 |
"80759 -0.621488 0.761285 0.000000 \n", |
|
|
7089 |
"3192 0.000000 1.021480 0.599318 \n", |
|
|
7090 |
"3192 0.000000 1.021480 0.599318 \n", |
|
|
7091 |
"387707 -0.610433 -0.577767 0.000000 \n", |
|
|
7092 |
"387707 -0.610433 -0.577767 0.000000 \n", |
|
|
7093 |
"79741 -0.588574 0.459432 0.000000 \n", |
|
|
7094 |
"79741 -0.588574 0.459432 0.269033 \n", |
|
|
7095 |
"\n", |
|
|
7096 |
"[77 rows x 375 columns]" |
|
|
7097 |
] |
|
|
7098 |
}, |
|
|
7099 |
"execution_count": 36, |
|
|
7100 |
"metadata": {}, |
|
|
7101 |
"output_type": "execute_result" |
|
|
7102 |
} |
|
|
7103 |
], |
|
|
7104 |
"source": [ |
|
|
7105 |
"dups = list(set(pdx[pdx.index.duplicated(keep=False)].index.values))\n", |
|
|
7106 |
"pdx.loc[dups,:]" |
|
|
7107 |
] |
|
|
7108 |
}, |
|
|
7109 |
{ |
|
|
7110 |
"cell_type": "code", |
|
|
7111 |
"execution_count": 37, |
|
|
7112 |
"metadata": {}, |
|
|
7113 |
"outputs": [ |
|
|
7114 |
{ |
|
|
7115 |
"name": "stdout", |
|
|
7116 |
"output_type": "stream", |
|
|
7117 |
"text": [ |
|
|
7118 |
"37 duplicated IDs in 77 rows found.\n", |
|
|
7119 |
"duplicate rows removed due to low correlation of duplicated profiles 4\n", |
|
|
7120 |
"Merged 73 duplicated rows into 35 rows\n" |
|
|
7121 |
] |
|
|
7122 |
} |
|
|
7123 |
], |
|
|
7124 |
"source": [ |
|
|
7125 |
"# most of these dupliates correspond to genes merged in the current assembly, e.g. gene - gene-AS\n", |
|
|
7126 |
"pdx = handle_dups(pdx,corr_thr = 0.75)" |
|
|
7127 |
] |
|
|
7128 |
}, |
|
|
7129 |
{ |
|
|
7130 |
"cell_type": "code", |
|
|
7131 |
"execution_count": 38, |
|
|
7132 |
"metadata": {}, |
|
|
7133 |
"outputs": [], |
|
|
7134 |
"source": [ |
|
|
7135 |
"pdx = pdx.T.sort_index().T\n", |
|
|
7136 |
"pdx.to_csv(preprocessed_dir+\"/\"+\"PDX\"+\".Segment_Mean.CNA.tsv\",\n", |
|
|
7137 |
" sep = \"\\t\",header=True,index=True)" |
|
|
7138 |
] |
|
|
7139 |
}, |
|
|
7140 |
{ |
|
|
7141 |
"cell_type": "markdown", |
|
|
7142 |
"metadata": {}, |
|
|
7143 |
"source": [ |
|
|
7144 |
"### Evaluation of the results\n", |
|
|
7145 |
"1). How many common genes between four datasets?\n", |
|
|
7146 |
"\n", |
|
|
7147 |
"2). Do CNA profiles of the same cell line from GDSC and CCLE correlate?\n", |
|
|
7148 |
"\n", |
|
|
7149 |
"3). Do CNA profiles of the same cancer type from TCGA and PDX look similar?\n", |
|
|
7150 |
"\n" |
|
|
7151 |
] |
|
|
7152 |
}, |
|
|
7153 |
{ |
|
|
7154 |
"cell_type": "code", |
|
|
7155 |
"execution_count": null, |
|
|
7156 |
"metadata": {}, |
|
|
7157 |
"outputs": [], |
|
|
7158 |
"source": [] |
|
|
7159 |
}, |
|
|
7160 |
{ |
|
|
7161 |
"cell_type": "code", |
|
|
7162 |
"execution_count": 39, |
|
|
7163 |
"metadata": {}, |
|
|
7164 |
"outputs": [ |
|
|
7165 |
{ |
|
|
7166 |
"ename": "IOError", |
|
|
7167 |
"evalue": "File /home/olya/SFU/Hossein/v1/preprocessed/CNA/BRCA.Segment_Mean.CNA.tsv does not exist", |
|
|
7168 |
"output_type": "error", |
|
|
7169 |
"traceback": [ |
|
|
7170 |
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", |
|
|
7171 |
"\u001b[0;31mIOError\u001b[0m Traceback (most recent call last)", |
|
|
7172 |
"\u001b[0;32m<ipython-input-39-1f476096b0ec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m### 1). How many common genes between four datasets?\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;31m# we take BRCA from TCGA because\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mtcga\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpreprocessed_dir\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m\"BRCA\"\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m\".Segment_Mean.CNA.tsv\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0msep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\\t\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindex_col\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0;31m#print(tcga.head(3))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mgdsc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpreprocessed_dir\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m\"GDSC\"\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m\".Segment_Mean.CNA.tsv\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0msep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\\t\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindex_col\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7173 |
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36mparser_f\u001b[0;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, doublequote, delim_whitespace, low_memory, memory_map, float_precision)\u001b[0m\n\u001b[1;32m 676\u001b[0m skip_blank_lines=skip_blank_lines)\n\u001b[1;32m 677\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 678\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 679\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 680\u001b[0m \u001b[0mparser_f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7174 |
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m 438\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 439\u001b[0m \u001b[0;31m# Create the parser.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 440\u001b[0;31m \u001b[0mparser\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTextFileReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 441\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 442\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mchunksize\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0miterator\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7175 |
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, f, engine, **kwds)\u001b[0m\n\u001b[1;32m 785\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 786\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 787\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mengine\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 788\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 789\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7176 |
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m_make_engine\u001b[0;34m(self, engine)\u001b[0m\n\u001b[1;32m 1012\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mengine\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'c'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1013\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'c'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1014\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCParserWrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1015\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1016\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'python'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7177 |
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, src, **kwds)\u001b[0m\n\u001b[1;32m 1706\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'usecols'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0musecols\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1707\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1708\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparsers\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mTextReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msrc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1709\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1710\u001b[0m \u001b[0mpassed_names\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnames\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
|
|
7178 |
"\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.__cinit__\u001b[0;34m()\u001b[0m\n", |
|
|
7179 |
"\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._setup_parser_source\u001b[0;34m()\u001b[0m\n", |
|
|
7180 |
"\u001b[0;31mIOError\u001b[0m: File /home/olya/SFU/Hossein/v1/preprocessed/CNA/BRCA.Segment_Mean.CNA.tsv does not exist" |
|
|
7181 |
] |
|
|
7182 |
} |
|
|
7183 |
], |
|
|
7184 |
"source": [ |
|
|
7185 |
"### 1). How many common genes between four datasets?\n", |
|
|
7186 |
"# we take BRCA from TCGA because \n", |
|
|
7187 |
"tcga = pd.read_csv(preprocessed_dir+\"BRCA\"+\".Segment_Mean.CNA.tsv\",sep = \"\\t\", index_col=0)\n", |
|
|
7188 |
"#print(tcga.head(3))\n", |
|
|
7189 |
"gdsc = pd.read_csv(preprocessed_dir+\"GDSC\"+\".Segment_Mean.CNA.tsv\",sep = \"\\t\", index_col=0)\n", |
|
|
7190 |
"#print(tcga.head(3))" |
|
|
7191 |
] |
|
|
7192 |
}, |
|
|
7193 |
{ |
|
|
7194 |
"cell_type": "code", |
|
|
7195 |
"execution_count": null, |
|
|
7196 |
"metadata": {}, |
|
|
7197 |
"outputs": [], |
|
|
7198 |
"source": [ |
|
|
7199 |
"### distribution of logR values in GDSC and CCLE \n", |
|
|
7200 |
"cn_values_gdsc = []\n", |
|
|
7201 |
"for row in df.iterrows():\n", |
|
|
7202 |
" cn_values_gdsc += list(row[1].values)\n", |
|
|
7203 |
"cn_values_ccle = []\n", |
|
|
7204 |
"for row in cna_table.iterrows():\n", |
|
|
7205 |
" cn_values_ccle+= list(row[1].values)\n", |
|
|
7206 |
"\n", |
|
|
7207 |
"cn_values_gdsc = sorted (cn_values_gdsc)\n", |
|
|
7208 |
"cn_values_ccle = sorted (cn_values_ccle)\n", |
|
|
7209 |
"plt.figure(figsize=(20,5))\n", |
|
|
7210 |
"plt.subplot(121)\n", |
|
|
7211 |
"tmp = plt.hist(cn_values_gdsc,bins=100,density = True,range=(-5,4))\n", |
|
|
7212 |
"plt.title(\"GDSC\")\n", |
|
|
7213 |
"plt.subplot(122)\n", |
|
|
7214 |
"tmp = plt.hist(cn_values_ccle,bins=100,density = True, range=(-5,4))\n", |
|
|
7215 |
"plt.title(\"CCLE\")" |
|
|
7216 |
] |
|
|
7217 |
} |
|
|
7218 |
], |
|
|
7219 |
"metadata": { |
|
|
7220 |
"kernelspec": { |
|
|
7221 |
"display_name": "Python 2", |
|
|
7222 |
"language": "python", |
|
|
7223 |
"name": "python2" |
|
|
7224 |
}, |
|
|
7225 |
"language_info": { |
|
|
7226 |
"codemirror_mode": { |
|
|
7227 |
"name": "ipython", |
|
|
7228 |
"version": 2 |
|
|
7229 |
}, |
|
|
7230 |
"file_extension": ".py", |
|
|
7231 |
"mimetype": "text/x-python", |
|
|
7232 |
"name": "python", |
|
|
7233 |
"nbconvert_exporter": "python", |
|
|
7234 |
"pygments_lexer": "ipython2", |
|
|
7235 |
"version": "2.7.15" |
|
|
7236 |
} |
|
|
7237 |
}, |
|
|
7238 |
"nbformat": 4, |
|
|
7239 |
"nbformat_minor": 2 |
|
|
7240 |
} |