Datasets
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Downloads: 1
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "a9b12fb4-8de2-4590-964d-9315e3a3cc97",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Seed set to 42\n"
]
}
],
"source": [
"import os\n",
"import flexynesis\n",
"import torch\n",
"import numpy as np\n",
"import pandas as pd"
]
},
{
"cell_type": "markdown",
"id": "59440372-485a-4229-8846-531cc9912904",
"metadata": {},
"source": [
"https://www.cbioportal.org/study/summary?id=msk_impact_2017"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "32f3cbf5-3af6-47a5-9fdd-6f6d89c51e39",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Downloading https://cbioportal-datahub.s3.amazonaws.com/msk_impact_2017.tar.gz...\n",
"Extracting msk_impact_2017.tar.gz...\n",
" Available Data Files\n",
" data_clinical_sample.txt\n",
" data_mutations.txt\n",
" data_cna.txt\n",
"data_gene_panel_matrix.txt\n",
" data_clinical_patient.txt\n",
" data_sv.txt\n",
"\n",
"\n",
"Please select a list of files to import. Example:\n",
" get_cbioportal_data('study_id', files={'mut': 'data_mutations.txt', 'clin': 'data_clinical_patient.txt'})\n"
]
}
],
"source": [
"cbio = flexynesis.CBioPortalData('msk_impact_2017')\n",
"cbio.get_cbioportal_data(cbio.study_id)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "13d7e87c-c558-427a-a374-1ee0467e82c6",
"metadata": {},
"outputs": [],
"source": [
"cna = pd.read_csv('./msk_impact_2017/data_cna.txt', delimiter='\\t')"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "9b849acd-2b7d-4316-a065-9e3f68eec7a3",
"metadata": {},
"outputs": [
{
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"0 ABL1 0 0 0 \n",
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"4 0 0 0 0 \n",
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" P-0012622-T01-IM5 \n",
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"\n",
"[5 rows x 10946 columns]"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cna.head()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "552617dd-d21c-4084-b57f-7e13e900326f",
"metadata": {},
"outputs": [],
"source": [
"mut = pd.read_csv('./msk_impact_2017/data_mutations.txt', delimiter='\\t', skiprows=1)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "a9723f14-7ebe-45d2-bc7f-b9e355dcac63",
"metadata": {},
"outputs": [
{
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"<table border=\"1\" class=\"dataframe\">\n",
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" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Hugo_Symbol</th>\n",
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" <td>NM_005921.1</td>\n",
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" <td>ENST00000261937.6:c.3971G>T</td>\n",
" <td>p.Arg1324Leu</td>\n",
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],
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" Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position \\\n",
"0 SPEN NaN NaN GRCh37 1 16265908 \n",
"1 ALK NaN NaN GRCh37 2 29543736 \n",
"2 PDCD1 NaN NaN GRCh37 2 242793433 \n",
"3 MAP3K1 NaN NaN GRCh37 5 56177843 \n",
"4 FLT4 NaN NaN GRCh37 5 180030313 \n",
"\n",
" End_Position Strand Consequence Variant_Classification ... \\\n",
"0 16265908 + missense_variant Missense_Mutation ... \n",
"1 29543736 + missense_variant Missense_Mutation ... \n",
"2 242793433 + missense_variant Missense_Mutation ... \n",
"3 56177843 + missense_variant Missense_Mutation ... \n",
"4 180030313 + missense_variant Missense_Mutation ... \n",
"\n",
" n_alt_count HGVSc HGVSp HGVSp_Short \\\n",
"0 NaN ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F \n",
"1 NaN ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A \n",
"2 NaN ENST00000334409.5:c.644C>T p.Ala215Val p.A215V \n",
"3 NaN ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C \n",
"4 NaN ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L \n",
"\n",
" Transcript_ID RefSeq Protein_position Codons Hotspot \\\n",
"0 ENST00000375759 NM_015001.2 3661.0 Att/Ttt 0 \n",
"1 ENST00000389048 NM_004304.4 476.0 gTg/gCg 0 \n",
"2 ENST00000334409 NM_005018.2 215.0 gCc/gTc 0 \n",
"3 ENST00000399503 NM_005921.1 939.0 tCt/tGt 0 \n",
"4 ENST00000261937 NM_182925.4 1324.0 cGg/cTg 0 \n",
"\n",
" cDNA_change \n",
"0 c.10981A>T \n",
"1 c.1427T>C \n",
"2 c.644C>T \n",
"3 c.2816C>G \n",
"4 c.3971G>T \n",
"\n",
"[5 rows x 46 columns]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mut.head()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "8935fc81-691d-4370-be9e-1242d8f99510",
"metadata": {},
"outputs": [],
"source": [
"clin = pd.read_csv('./msk_impact_2017/data_clinical_sample.txt', delimiter='\\t', skiprows=4)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "967a9785-b1c8-42a5-b365-dcf625e9d596",
"metadata": {},
"outputs": [
{
"data": {
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" <td>P-0000023-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>454</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Peritoneum</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>PEMESO</td>\n",
" <td>Mesothelioma</td>\n",
" <td>Peritoneal Mesothelioma</td>\n",
" <td>Matched</td>\n",
" <td>5.545777</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>P-0000024</td>\n",
" <td>P-0000024-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>1016</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Lung</td>\n",
" <td>Tumor</td>\n",
" <td>UEC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Endometrioid Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>6.654932</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>P-0000025</td>\n",
" <td>P-0000025-T02-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>1147</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Peritoneum</td>\n",
" <td>Tumor</td>\n",
" <td>USC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Serous Carcinoma/Uterine Papillary Ser...</td>\n",
" <td>Matched</td>\n",
" <td>1.957439</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" PATIENT_ID SAMPLE_ID SAMPLE_COLLECTION_SOURCE \\\n",
"0 P-0000004 P-0000004-T01-IM3 Outside \n",
"1 P-0000015 P-0000015-T01-IM3 In-House \n",
"2 P-0000023 P-0000023-T01-IM3 In-House \n",
"3 P-0000024 P-0000024-T01-IM3 In-House \n",
"4 P-0000025 P-0000025-T02-IM5 In-House \n",
"\n",
" SPECIMEN_PRESERVATION_TYPE SPECIMEN_TYPE DNA_INPUT SAMPLE_COVERAGE \\\n",
"0 FFPE Biopsy 250.0 428 \n",
"1 FFPE Biopsy 198.0 281 \n",
"2 FFPE Biopsy 250.0 454 \n",
"3 FFPE Resection 250.0 1016 \n",
"4 FFPE Biopsy 250.0 1147 \n",
"\n",
" TUMOR_PURITY MATCHED_STATUS SAMPLE_TYPE PRIMARY_SITE METASTATIC_SITE \\\n",
"0 50.0 Matched Primary Breast Not Applicable \n",
"1 40.0 Matched Metastasis Breast Liver \n",
"2 30.0 Matched Primary Peritoneum Not Applicable \n",
"3 40.0 Matched Metastasis Uterus Lung \n",
"4 30.0 Matched Metastasis Uterus Peritoneum \n",
"\n",
" SAMPLE_CLASS ONCOTREE_CODE CANCER_TYPE \\\n",
"0 Tumor IDC Breast Cancer \n",
"1 Tumor IDC Breast Cancer \n",
"2 Tumor PEMESO Mesothelioma \n",
"3 Tumor UEC Endometrial Cancer \n",
"4 Tumor USC Endometrial Cancer \n",
"\n",
" CANCER_TYPE_DETAILED SOMATIC_STATUS \\\n",
"0 Breast Invasive Ductal Carcinoma Matched \n",
"1 Breast Invasive Ductal Carcinoma Matched \n",
"2 Peritoneal Mesothelioma Matched \n",
"3 Uterine Endometrioid Carcinoma Matched \n",
"4 Uterine Serous Carcinoma/Uterine Papillary Ser... Matched \n",
"\n",
" TMB_NONSYNONYMOUS \n",
"0 17.746485 \n",
"1 7.764087 \n",
"2 5.545777 \n",
"3 6.654932 \n",
"4 1.957439 "
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"clin.head()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "7ebdbd09-b49c-4199-8172-bd3d486fc7ef",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Importing data_mutations.txt...\n",
"Binarizing and converting data_mutations.txt to matrix...\n",
"Importing data_cna.txt...\n",
"Converting data_cna.txt to matrix...\n",
"Importing data_clinical_sample.txt...\n",
"{'mut': (414, 10129), 'cna': (410, 10945), 'clin': (10336, 17)}\n"
]
}
],
"source": [
"cbio.get_cbioportal_data(cbio.study_id, files={'mut': 'data_mutations.txt', 'cna': 'data_cna.txt', 'clin': 'data_clinical_sample.txt'})"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "c31984c3-4f1b-4b4b-a055-c889ab4e1d52",
"metadata": {},
"outputs": [],
"source": [
"data = cbio.data"
]
},
{
"cell_type": "code",
"execution_count": 21,
"id": "3b9f4c71-0b01-47d5-8ddc-7361fb4ed5ca",
"metadata": {},
"outputs": [
{
"data": {
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"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>SAMPLE_ID</th>\n",
" <th>SAMPLE_COLLECTION_SOURCE</th>\n",
" <th>SPECIMEN_PRESERVATION_TYPE</th>\n",
" <th>SPECIMEN_TYPE</th>\n",
" <th>DNA_INPUT</th>\n",
" <th>SAMPLE_COVERAGE</th>\n",
" <th>TUMOR_PURITY</th>\n",
" <th>MATCHED_STATUS</th>\n",
" <th>SAMPLE_TYPE</th>\n",
" <th>PRIMARY_SITE</th>\n",
" <th>METASTATIC_SITE</th>\n",
" <th>SAMPLE_CLASS</th>\n",
" <th>ONCOTREE_CODE</th>\n",
" <th>CANCER_TYPE</th>\n",
" <th>CANCER_TYPE_DETAILED</th>\n",
" <th>SOMATIC_STATUS</th>\n",
" <th>TMB_NONSYNONYMOUS</th>\n",
" </tr>\n",
" <tr>\n",
" <th>PATIENT_ID</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <tbody>\n",
" <tr>\n",
" <th>P-0000004</th>\n",
" <td>P-0000004-T01-IM3</td>\n",
" <td>Outside</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>428.0</td>\n",
" <td>50.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Breast</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>IDC</td>\n",
" <td>Breast Cancer</td>\n",
" <td>Breast Invasive Ductal Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>17.746485</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000015</th>\n",
" <td>P-0000015-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>198.0</td>\n",
" <td>281.0</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Breast</td>\n",
" <td>Liver</td>\n",
" <td>Tumor</td>\n",
" <td>IDC</td>\n",
" <td>Breast Cancer</td>\n",
" <td>Breast Invasive Ductal Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>7.764087</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000023</th>\n",
" <td>P-0000023-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>454.0</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Peritoneum</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>PEMESO</td>\n",
" <td>Mesothelioma</td>\n",
" <td>Peritoneal Mesothelioma</td>\n",
" <td>Matched</td>\n",
" <td>5.545777</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000024</th>\n",
" <td>P-0000024-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>1016.0</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Lung</td>\n",
" <td>Tumor</td>\n",
" <td>UEC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Endometrioid Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>6.654932</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000025</th>\n",
" <td>P-0000025-T02-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>1147.0</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Peritoneum</td>\n",
" <td>Tumor</td>\n",
" <td>USC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Serous Carcinoma/Uterine Papillary Ser...</td>\n",
" <td>Matched</td>\n",
" <td>1.957439</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" SAMPLE_ID SAMPLE_COLLECTION_SOURCE \\\n",
"PATIENT_ID \n",
"P-0000004 P-0000004-T01-IM3 Outside \n",
"P-0000015 P-0000015-T01-IM3 In-House \n",
"P-0000023 P-0000023-T01-IM3 In-House \n",
"P-0000024 P-0000024-T01-IM3 In-House \n",
"P-0000025 P-0000025-T02-IM5 In-House \n",
"\n",
" SPECIMEN_PRESERVATION_TYPE SPECIMEN_TYPE DNA_INPUT \\\n",
"PATIENT_ID \n",
"P-0000004 FFPE Biopsy 250.0 \n",
"P-0000015 FFPE Biopsy 198.0 \n",
"P-0000023 FFPE Biopsy 250.0 \n",
"P-0000024 FFPE Resection 250.0 \n",
"P-0000025 FFPE Biopsy 250.0 \n",
"\n",
" SAMPLE_COVERAGE TUMOR_PURITY MATCHED_STATUS SAMPLE_TYPE \\\n",
"PATIENT_ID \n",
"P-0000004 428.0 50.0 Matched Primary \n",
"P-0000015 281.0 40.0 Matched Metastasis \n",
"P-0000023 454.0 30.0 Matched Primary \n",
"P-0000024 1016.0 40.0 Matched Metastasis \n",
"P-0000025 1147.0 30.0 Matched Metastasis \n",
"\n",
" PRIMARY_SITE METASTATIC_SITE SAMPLE_CLASS ONCOTREE_CODE \\\n",
"PATIENT_ID \n",
"P-0000004 Breast Not Applicable Tumor IDC \n",
"P-0000015 Breast Liver Tumor IDC \n",
"P-0000023 Peritoneum Not Applicable Tumor PEMESO \n",
"P-0000024 Uterus Lung Tumor UEC \n",
"P-0000025 Uterus Peritoneum Tumor USC \n",
"\n",
" CANCER_TYPE \\\n",
"PATIENT_ID \n",
"P-0000004 Breast Cancer \n",
"P-0000015 Breast Cancer \n",
"P-0000023 Mesothelioma \n",
"P-0000024 Endometrial Cancer \n",
"P-0000025 Endometrial Cancer \n",
"\n",
" CANCER_TYPE_DETAILED SOMATIC_STATUS \\\n",
"PATIENT_ID \n",
"P-0000004 Breast Invasive Ductal Carcinoma Matched \n",
"P-0000015 Breast Invasive Ductal Carcinoma Matched \n",
"P-0000023 Peritoneal Mesothelioma Matched \n",
"P-0000024 Uterine Endometrioid Carcinoma Matched \n",
"P-0000025 Uterine Serous Carcinoma/Uterine Papillary Ser... Matched \n",
"\n",
" TMB_NONSYNONYMOUS \n",
"PATIENT_ID \n",
"P-0000004 17.746485 \n",
"P-0000015 7.764087 \n",
"P-0000023 5.545777 \n",
"P-0000024 6.654932 \n",
"P-0000025 1.957439 "
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data['clin'].head()"
]
},
{
"cell_type": "code",
"execution_count": 22,
"id": "00c3c4b7-bca0-4688-8204-6a6d82877f44",
"metadata": {},
"outputs": [],
"source": [
"data['clin'].index = data['clin'].SAMPLE_ID"
]
},
{
"cell_type": "code",
"execution_count": 23,
"id": "169441c4-9aea-475c-b4b6-59b1f29f4188",
"metadata": {},
"outputs": [],
"source": [
"counts = np.unique(list(data['clin'].PRIMARY_SITE), return_counts=True) "
]
},
{
"cell_type": "code",
"execution_count": 24,
"id": "35108027-7bbc-4a52-a4a2-f27ad26525db",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(array([' Lung', 'Abdomen', 'Abdominal Wall', 'Adnexa', 'Adrenal Gland',\n",
" 'Ampulla of Vater', 'Anal', 'Anorectal Junction', 'Anus',\n",
" 'Appendix', 'Arm', 'Ascending Colon', 'Auditory Canal', 'Axilla',\n",
" 'Back', 'Bile Duct', 'Bladder', 'Blood', 'Blood Vessel', 'Bone',\n",
" 'Bone Marrow', 'Bowel', 'Brain', 'Breast', 'Buttock',\n",
" 'Cancer of Unknown Primary', 'Cecum', 'Cervix', 'Cheek', 'Chest',\n",
" 'Chest Wall', 'Clivus', 'Colon', 'Colorectal NOS', 'Conjunctiva',\n",
" 'Descending Colon', 'Diaphragm', 'Duodenum', 'Duodenum-Jejunum',\n",
" 'Ear Canal', 'Ectopic Embryonic Rest', 'Epidural', 'Esophagus',\n",
" 'Ethmoid Sinus', 'Eye', 'Eyelid', 'Femoral Tendon', 'Femoral Vein',\n",
" 'Fibula', 'Foot', 'Forearm', 'Forehead', 'GE Junction',\n",
" 'Gallbladder', 'Gastric Wall', 'Groin', 'Hard palate', 'Heart',\n",
" 'Hip', 'Hypopharynx', 'Ileocecal Valve', 'Ileum', 'Intraabdominal',\n",
" 'Intrahepatic Bile Duct', 'Jejunum', 'Kidney', 'Knee', 'Larynx',\n",
" 'Leg', 'Liver', 'Lower Extremity', 'Lung', 'Lymph Node',\n",
" 'Lymph node', 'Major Salivary Gland', 'Mandible', 'Maxilla',\n",
" 'Maxillary Sinus', 'Mediastinum', 'Mesentery',\n",
" 'Minor Salivary Gland', 'Muscle', 'Nailbed', 'Nasal Cavity',\n",
" 'Nasopharynx', 'Neck', 'Nerve Sheath', 'Not available', 'Omentum',\n",
" 'Oral Cavity', 'Orbit', 'Oropharynx', 'Ovary', 'Palate',\n",
" 'Pancreas', 'Paraspinal', 'Parotid', 'Parotid Gland', 'Pelvis',\n",
" 'Penis', 'Peri-colic gutter', 'Perineal', 'Perineal mass',\n",
" 'Perineum', 'Peritoneum', 'Periurethra', 'Pharynx',\n",
" 'Pituitary Gland', 'Pituitary Mass', 'Pleura', 'Pleural Fluid',\n",
" 'Porto-cava mass', 'Prostate', 'Pubic Mass', 'Rectosigmoid Colon',\n",
" 'Rectum', 'Retroperitoneum', 'Rib', 'Sacral Mass', 'Sacrum',\n",
" 'Salivary Gland', 'Scalp', 'Sigmoid Colon', 'Sinonasal', 'Sinus',\n",
" 'Skin', 'Skull', 'Skull Base', 'Small Bowel', 'Small Intestine',\n",
" 'Soft Palate', 'Soft Tissue', 'Spinal Cord', 'Spinal cord',\n",
" 'Spine', 'Spleen', 'Stomach', 'Submandibular Gland',\n",
" 'Subungual Toe', 'Sweat Gland', 'Testis', 'Thigh',\n",
" 'Thoracic Spine', 'Thymus', 'Thyroid', 'Tongue', 'Tonsil',\n",
" 'Trachea', 'Transverse Colon', 'Umbilical Mass', 'Unknown',\n",
" 'Upper Extremity', 'Upper Tract', 'Urethra', 'Uterus', 'Vagina',\n",
" 'Vulva', 'nan'], dtype='<U32'),\n",
" array([ 1, 19, 3, 1, 78, 15, 1, 1, 36, 81, 4,\n",
" 102, 1, 2, 3, 47, 323, 1, 5, 88, 1, 1,\n",
" 582, 1258, 4, 211, 137, 49, 1, 1, 12, 1, 13,\n",
" 16, 4, 53, 1, 20, 1, 1, 1, 4, 125, 3,\n",
" 51, 5, 1, 1, 1, 8, 1, 1, 38, 51, 1,\n",
" 6, 1, 7, 1, 3, 2, 11, 10, 1, 11, 330,\n",
" 2, 20, 17, 255, 33, 1673, 19, 87, 49, 1, 8,\n",
" 1, 55, 5, 24, 4, 3, 1, 21, 13, 1, 27,\n",
" 3, 47, 1, 40, 240, 1, 497, 1, 2, 11, 27,\n",
" 8, 1, 1, 1, 1, 14, 1, 6, 1, 1, 81,\n",
" 1, 1, 622, 1, 95, 255, 80, 1, 2, 1, 8,\n",
" 11, 266, 10, 8, 326, 1, 1, 61, 1, 1, 148,\n",
" 1, 1, 3, 2, 237, 4, 1, 1, 232, 9, 1,\n",
" 17, 223, 11, 9, 6, 87, 1, 3, 9, 79, 9,\n",
" 306, 13, 10, 1]))"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"counts"
]
},
{
"cell_type": "code",
"execution_count": 25,
"id": "118bc876-c86d-4bc4-a8b5-8e18487b083e",
"metadata": {},
"outputs": [],
"source": [
"cancer_types = counts[0][np.where(counts[1] > 300)]"
]
},
{
"cell_type": "code",
"execution_count": 26,
"id": "bdf59175-9ffb-4728-8117-e4ba70f039af",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['Bladder', 'Brain', 'Breast', 'Kidney', 'Lung', 'Pancreas',\n",
" 'Prostate', 'Skin', 'Uterus'], dtype='<U32')"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cancer_types"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "66cffb9b-2308-4ed3-a474-2f720dd54cf4",
"metadata": {},
"outputs": [],
"source": [
"clin_subset = data['clin'][data['clin']['PRIMARY_SITE'].isin(cancer_types)]"
]
},
{
"cell_type": "code",
"execution_count": 32,
"id": "11056225-b3fa-4f34-a3ca-7381786ca0de",
"metadata": {},
"outputs": [],
"source": [
"data['clin'] = clin_subset"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "f38e6f68-deab-440c-98d6-5556078f06e5",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(5917, 17)"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data['clin'].shape"
]
},
{
"cell_type": "code",
"execution_count": 31,
"id": "4488ad3d-c7eb-4b0a-9ce4-17883cca743a",
"metadata": {},
"outputs": [
{
"data": {
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" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>P-0000004-T01-IM3</th>\n",
" <td>P-0000004-T01-IM3</td>\n",
" <td>Outside</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>428.0</td>\n",
" <td>50.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Breast</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>IDC</td>\n",
" <td>Breast Cancer</td>\n",
" <td>Breast Invasive Ductal Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>17.746485</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000015-T01-IM3</th>\n",
" <td>P-0000015-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>198.0</td>\n",
" <td>281.0</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Breast</td>\n",
" <td>Liver</td>\n",
" <td>Tumor</td>\n",
" <td>IDC</td>\n",
" <td>Breast Cancer</td>\n",
" <td>Breast Invasive Ductal Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>7.764087</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000024-T01-IM3</th>\n",
" <td>P-0000024-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>1016.0</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Lung</td>\n",
" <td>Tumor</td>\n",
" <td>UEC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Endometrioid Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>6.654932</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000025-T02-IM5</th>\n",
" <td>P-0000025-T02-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>1147.0</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Peritoneum</td>\n",
" <td>Tumor</td>\n",
" <td>USC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Serous Carcinoma/Uterine Papillary Ser...</td>\n",
" <td>Matched</td>\n",
" <td>1.957439</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0000026-T01-IM3</th>\n",
" <td>P-0000026-T01-IM3</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Cytology</td>\n",
" <td>250.0</td>\n",
" <td>1222.0</td>\n",
" <td>10.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Uterus</td>\n",
" <td>Pelvis</td>\n",
" <td>Tumor</td>\n",
" <td>UEC</td>\n",
" <td>Endometrial Cancer</td>\n",
" <td>Uterine Endometrioid Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>4.436621</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0012405-T01-IM5</th>\n",
" <td>P-0012405-T01-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>832.0</td>\n",
" <td>10.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Pancreas</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>PAAD</td>\n",
" <td>Pancreatic Cancer</td>\n",
" <td>Pancreatic Adenocarcinoma</td>\n",
" <td>Matched</td>\n",
" <td>0.978720</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0012434-T01-IM5</th>\n",
" <td>P-0012434-T01-IM5</td>\n",
" <td>Outside</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>250.0</td>\n",
" <td>769.0</td>\n",
" <td>70.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Brain</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>ODG</td>\n",
" <td>Glioma</td>\n",
" <td>Oligodendroglioma</td>\n",
" <td>Matched</td>\n",
" <td>2.936159</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0012442-T01-IM5</th>\n",
" <td>P-0012442-T01-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>815.0</td>\n",
" <td>30.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Pancreas</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>PAAD</td>\n",
" <td>Pancreatic Cancer</td>\n",
" <td>Pancreatic Adenocarcinoma</td>\n",
" <td>Matched</td>\n",
" <td>1.957439</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0012500-T01-IM5</th>\n",
" <td>P-0012500-T01-IM5</td>\n",
" <td>In-House</td>\n",
" <td>FFPE</td>\n",
" <td>Resection</td>\n",
" <td>250.0</td>\n",
" <td>812.0</td>\n",
" <td>50.0</td>\n",
" <td>Matched</td>\n",
" <td>Primary</td>\n",
" <td>Breast</td>\n",
" <td>Not Applicable</td>\n",
" <td>Tumor</td>\n",
" <td>BRCA</td>\n",
" <td>Breast Cancer</td>\n",
" <td>Invasive Breast Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>1.957439</td>\n",
" </tr>\n",
" <tr>\n",
" <th>P-0012557-T01-IM5</th>\n",
" <td>P-0012557-T01-IM5</td>\n",
" <td>Outside</td>\n",
" <td>FFPE</td>\n",
" <td>Biopsy</td>\n",
" <td>90.0</td>\n",
" <td>297.0</td>\n",
" <td>40.0</td>\n",
" <td>Matched</td>\n",
" <td>Metastasis</td>\n",
" <td>Bladder</td>\n",
" <td>Soft Tissue</td>\n",
" <td>Tumor</td>\n",
" <td>BLCA</td>\n",
" <td>Bladder Cancer</td>\n",
" <td>Bladder Urothelial Carcinoma</td>\n",
" <td>Matched</td>\n",
" <td>14.680795</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5917 rows × 17 columns</p>\n",
"</div>"
],
"text/plain": [
" SAMPLE_ID SAMPLE_COLLECTION_SOURCE \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 P-0000004-T01-IM3 Outside \n",
"P-0000015-T01-IM3 P-0000015-T01-IM3 In-House \n",
"P-0000024-T01-IM3 P-0000024-T01-IM3 In-House \n",
"P-0000025-T02-IM5 P-0000025-T02-IM5 In-House \n",
"P-0000026-T01-IM3 P-0000026-T01-IM3 In-House \n",
"... ... ... \n",
"P-0012405-T01-IM5 P-0012405-T01-IM5 In-House \n",
"P-0012434-T01-IM5 P-0012434-T01-IM5 Outside \n",
"P-0012442-T01-IM5 P-0012442-T01-IM5 In-House \n",
"P-0012500-T01-IM5 P-0012500-T01-IM5 In-House \n",
"P-0012557-T01-IM5 P-0012557-T01-IM5 Outside \n",
"\n",
" SPECIMEN_PRESERVATION_TYPE SPECIMEN_TYPE DNA_INPUT \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 FFPE Biopsy 250.0 \n",
"P-0000015-T01-IM3 FFPE Biopsy 198.0 \n",
"P-0000024-T01-IM3 FFPE Resection 250.0 \n",
"P-0000025-T02-IM5 FFPE Biopsy 250.0 \n",
"P-0000026-T01-IM3 FFPE Cytology 250.0 \n",
"... ... ... ... \n",
"P-0012405-T01-IM5 FFPE Resection 250.0 \n",
"P-0012434-T01-IM5 FFPE Biopsy 250.0 \n",
"P-0012442-T01-IM5 FFPE Resection 250.0 \n",
"P-0012500-T01-IM5 FFPE Resection 250.0 \n",
"P-0012557-T01-IM5 FFPE Biopsy 90.0 \n",
"\n",
" SAMPLE_COVERAGE TUMOR_PURITY MATCHED_STATUS SAMPLE_TYPE \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 428.0 50.0 Matched Primary \n",
"P-0000015-T01-IM3 281.0 40.0 Matched Metastasis \n",
"P-0000024-T01-IM3 1016.0 40.0 Matched Metastasis \n",
"P-0000025-T02-IM5 1147.0 30.0 Matched Metastasis \n",
"P-0000026-T01-IM3 1222.0 10.0 Matched Metastasis \n",
"... ... ... ... ... \n",
"P-0012405-T01-IM5 832.0 10.0 Matched Primary \n",
"P-0012434-T01-IM5 769.0 70.0 Matched Primary \n",
"P-0012442-T01-IM5 815.0 30.0 Matched Primary \n",
"P-0012500-T01-IM5 812.0 50.0 Matched Primary \n",
"P-0012557-T01-IM5 297.0 40.0 Matched Metastasis \n",
"\n",
" PRIMARY_SITE METASTATIC_SITE SAMPLE_CLASS ONCOTREE_CODE \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 Breast Not Applicable Tumor IDC \n",
"P-0000015-T01-IM3 Breast Liver Tumor IDC \n",
"P-0000024-T01-IM3 Uterus Lung Tumor UEC \n",
"P-0000025-T02-IM5 Uterus Peritoneum Tumor USC \n",
"P-0000026-T01-IM3 Uterus Pelvis Tumor UEC \n",
"... ... ... ... ... \n",
"P-0012405-T01-IM5 Pancreas Not Applicable Tumor PAAD \n",
"P-0012434-T01-IM5 Brain Not Applicable Tumor ODG \n",
"P-0012442-T01-IM5 Pancreas Not Applicable Tumor PAAD \n",
"P-0012500-T01-IM5 Breast Not Applicable Tumor BRCA \n",
"P-0012557-T01-IM5 Bladder Soft Tissue Tumor BLCA \n",
"\n",
" CANCER_TYPE \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 Breast Cancer \n",
"P-0000015-T01-IM3 Breast Cancer \n",
"P-0000024-T01-IM3 Endometrial Cancer \n",
"P-0000025-T02-IM5 Endometrial Cancer \n",
"P-0000026-T01-IM3 Endometrial Cancer \n",
"... ... \n",
"P-0012405-T01-IM5 Pancreatic Cancer \n",
"P-0012434-T01-IM5 Glioma \n",
"P-0012442-T01-IM5 Pancreatic Cancer \n",
"P-0012500-T01-IM5 Breast Cancer \n",
"P-0012557-T01-IM5 Bladder Cancer \n",
"\n",
" CANCER_TYPE_DETAILED \\\n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 Breast Invasive Ductal Carcinoma \n",
"P-0000015-T01-IM3 Breast Invasive Ductal Carcinoma \n",
"P-0000024-T01-IM3 Uterine Endometrioid Carcinoma \n",
"P-0000025-T02-IM5 Uterine Serous Carcinoma/Uterine Papillary Ser... \n",
"P-0000026-T01-IM3 Uterine Endometrioid Carcinoma \n",
"... ... \n",
"P-0012405-T01-IM5 Pancreatic Adenocarcinoma \n",
"P-0012434-T01-IM5 Oligodendroglioma \n",
"P-0012442-T01-IM5 Pancreatic Adenocarcinoma \n",
"P-0012500-T01-IM5 Invasive Breast Carcinoma \n",
"P-0012557-T01-IM5 Bladder Urothelial Carcinoma \n",
"\n",
" SOMATIC_STATUS TMB_NONSYNONYMOUS \n",
"SAMPLE_ID \n",
"P-0000004-T01-IM3 Matched 17.746485 \n",
"P-0000015-T01-IM3 Matched 7.764087 \n",
"P-0000024-T01-IM3 Matched 6.654932 \n",
"P-0000025-T02-IM5 Matched 1.957439 \n",
"P-0000026-T01-IM3 Matched 4.436621 \n",
"... ... ... \n",
"P-0012405-T01-IM5 Matched 0.978720 \n",
"P-0012434-T01-IM5 Matched 2.936159 \n",
"P-0012442-T01-IM5 Matched 1.957439 \n",
"P-0012500-T01-IM5 Matched 1.957439 \n",
"P-0012557-T01-IM5 Matched 14.680795 \n",
"\n",
"[5917 rows x 17 columns]"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data['clin']"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "00447551-ed7c-48b5-b862-e7b1f430f713",
"metadata": {},
"outputs": [],
"source": [
"cbio.data = data"
]
},
{
"cell_type": "code",
"execution_count": 34,
"id": "787cd400-06de-4e90-95bf-0471a1124ad8",
"metadata": {},
"outputs": [],
"source": [
"dat_split = cbio.split_data()"
]
},
{
"cell_type": "code",
"execution_count": 35,
"id": "83b1997d-33b8-46c5-ab40-f8a4af21b92e",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'mut': (414, 1696), 'cna': (410, 1775), 'clin': (1775, 17)}"
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"{x: dat_split['test'][x].shape for x in dat_split['test'].keys()}"
]
},
{
"cell_type": "code",
"execution_count": 36,
"id": "54d4b72b-4992-4367-8f14-d5d6f950c8fb",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'mut': (414, 3918), 'cna': (410, 4142), 'clin': (4142, 17)}"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"{x: dat_split['train'][x].shape for x in dat_split['train'].keys()}"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "d72aaa38-3ae6-45ba-8f85-c3cd790a4c6b",
"metadata": {},
"outputs": [],
"source": [
"cbio.print_dataset(dat_split, 'msk_impact')"
]
},
{
"cell_type": "code",
"execution_count": 39,
"id": "4418a4fc-b060-4b55-bcb9-02626245d72e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"[INFO] ================= Importing Data =================\n",
"[INFO] Validating data folders...\n",
"\n",
"[INFO] ----------------- Reading Data ----------------- \n",
"[INFO] Importing msk_impact/train/cna.csv...\n",
"[INFO] Importing msk_impact/train/mut.csv...\n",
"[INFO] Importing msk_impact/train/clin.csv...\n",
"\n",
"[INFO] ----------------- Reading Data ----------------- \n",
"[INFO] Importing msk_impact/test/cna.csv...\n",
"[INFO] Importing msk_impact/test/mut.csv...\n",
"[INFO] Importing msk_impact/test/clin.csv...\n",
"\n",
"[INFO] ----------------- Checking for problems with the input data ----------------- \n",
"\n",
"[WARNING] Warnings:\n",
"\n",
"[WARNING] 1. Warning: Some sample labels in train/clin.csv are missing in train/mut.csv: {'P-0006147-T02-IM5', 'P-0001837-T01-IM3', 'P-0007050-T01-IM5', 'P-0007211-T01-IM5', 'P-0003993-T01-IM5', 'P-0008335-T01-IM5', 'P-0005909-T01-IM5', 'P-0006185-T01-IM5', 'P-0009472-T01-IM5', 'P-0004976-T01-IM5', 'P-0000350-T01-IM3', 'P-0008072-T01-IM5', 'P-0000544-T01-IM3', 'P-0008054-T01-IM5', 'P-0005278-T01-IM5', 'P-0005321-T01-IM5', 'P-0000266-T01-IM3', 'P-0003622-T01-IM5', 'P-0004345-T01-IM5', 'P-0004884-T01-IM5', 'P-0010683-T01-IM5', 'P-0006278-T01-IM5', 'P-0002807-T01-IM3', 'P-0009796-T02-IM5', 'P-0008208-T01-IM5', 'P-0011424-T01-IM5', 'P-0003684-T01-IM5', 'P-0007350-T01-IM5', 'P-0004467-T01-IM5', 'P-0003912-T01-IM3', 'P-0006573-T01-IM5', 'P-0011037-T01-IM5', 'P-0001060-T01-IM3', 'P-0011525-T01-IM5', 'P-0000808-T01-IM3', 'P-0001032-T01-IM3', 'P-0001988-T01-IM3', 'P-0006299-T01-IM5', 'P-0005513-T01-IM5', 'P-0001818-T01-IM3', 'P-0007424-T01-IM5', 'P-0002101-T01-IM3', 'P-0011214-T01-IM5', 'P-0011548-T01-IM5', 'P-0004452-T01-IM5', 'P-0005596-T01-IM5', 'P-0004532-T01-IM5', 'P-0001604-T01-IM3', 'P-0011501-T01-IM5', 'P-0003801-T01-IM5', 'P-0010842-T01-IM5', 'P-0012131-T01-IM5', 'P-0004516-T01-IM5', 'P-0002981-T01-IM3', 'P-0002283-T01-IM3', 'P-0005689-T01-IM5', 'P-0001838-T01-IM3', 'P-0001537-T01-IM3', 'P-0011251-T01-IM5', 'P-0010179-T01-IM5', 'P-0004333-T01-IM5', 'P-0012136-T01-IM5', 'P-0006549-T01-IM5', 'P-0011475-T01-IM5', 'P-0001552-T02-IM5', 'P-0003356-T01-IM5', 'P-0007662-T01-IM5', 'P-0001117-T01-IM3', 'P-0000116-T01-IM3', 'P-0003605-T01-IM5', 'P-0002082-T01-IM3', 'P-0000990-T02-IM3', 'P-0012141-T01-IM5', 'P-0001713-T01-IM3', 'P-0006313-T01-IM5', 'P-0004428-T01-IM5', 'P-0000479-T01-IM3', 'P-0006389-T01-IM5', 'P-0001429-T01-IM3', 'P-0010945-T01-IM5', 'P-0005834-T01-IM5', 'P-0005438-T01-IM5', 'P-0003470-T01-IM5', 'P-0007770-T01-IM5', 'P-0012190-T01-IM5', 'P-0002722-T01-IM3', 'P-0011311-T01-IM5', 'P-0006401-T02-IM5', 'P-0009947-T01-IM5', 'P-0005193-T01-IM5', 'P-0005052-T01-IM5', 'P-0003606-T01-IM5', 'P-0007647-T01-IM5', 'P-0005108-T01-IM5', 'P-0000638-T01-IM3', 'P-0001645-T01-IM3', 'P-0001737-T01-IM3', 'P-0001413-T01-IM3', 'P-0002481-T01-IM3', 'P-0009338-T01-IM5', 'P-0001138-T01-IM3', 'P-0005638-T01-IM5', 'P-0002942-T01-IM3', 'P-0009073-T01-IM5', 'P-0002735-T01-IM3', 'P-0006673-T01-IM5', 'P-0004343-T01-IM5', 'P-0000962-T01-IM3', 'P-0010029-T01-IM5', 'P-0008289-T01-IM5', 'P-0005649-T01-IM5', 'P-0011134-T01-IM5', 'P-0005557-T01-IM5', 'P-0007915-T01-IM5', 'P-0009926-T01-IM5', 'P-0012195-T01-IM5', 'P-0009444-T01-IM5', 'P-0001576-T01-IM3', 'P-0002583-T01-IM3', 'P-0012029-T01-IM5', 'P-0005387-T01-IM5', 'P-0004717-T01-IM5', 'P-0005901-T01-IM5', 'P-0003667-T01-IM5', 'P-0003061-T01-IM3', 'P-0002223-T01-IM3', 'P-0010808-T01-IM5', 'P-0002895-T01-IM3', 'P-0003001-T01-IM3', 'P-0010182-T01-IM5', 'P-0001694-T01-IM3', 'P-0000872-T01-IM3', 'P-0002024-T01-IM3', 'P-0010897-T01-IM5', 'P-0002360-T01-IM3', 'P-0010806-T01-IM5', 'P-0006893-T01-IM5', 'P-0003448-T01-IM5', 'P-0011019-T01-IM5', 'P-0003626-T01-IM5', 'P-0009077-T01-IM5', 'P-0004943-T01-IM5', 'P-0006311-T01-IM5', 'P-0000998-T01-IM3', 'P-0005086-T01-IM5', 'P-0005914-T01-IM5', 'P-0011576-T01-IM5', 'P-0004816-T01-IM5', 'P-0003677-T01-IM5', 'P-0004947-T01-IM5', 'P-0012213-T01-IM5', 'P-0003173-T01-IM5', 'P-0006346-T01-IM5', 'P-0000421-T01-IM3', 'P-0007098-T01-IM5', 'P-0011095-T01-IM5', 'P-0012062-T01-IM5', 'P-0000521-T01-IM3', 'P-0001563-T01-IM3', 'P-0011035-T01-IM5', 'P-0001606-T01-IM3', 'P-0003294-T01-IM5', 'P-0009176-T01-IM5', 'P-0012271-T01-IM5', 'P-0002431-T01-IM3', 'P-0007042-T01-IM5', 'P-0002661-T01-IM3', 'P-0008731-T01-IM5', 'P-0009440-T01-IM5', 'P-0007106-T01-IM5', 'P-0009562-T01-IM5', 'P-0004653-T01-IM5', 'P-0004576-T01-IM5', 'P-0002538-T01-IM3', 'P-0000689-T01-IM3', 'P-0012159-T01-IM5', 'P-0011382-T01-IM5', 'P-0003546-T01-IM5', 'P-0003411-T01-IM5', 'P-0003806-T01-IM5', 'P-0001839-T01-IM3', 'P-0001206-T01-IM3', 'P-0002217-T02-IM3', 'P-0010076-T01-IM5', 'P-0009241-T01-IM5', 'P-0005590-T01-IM5', 'P-0005095-T01-IM5', 'P-0012275-T01-IM5', 'P-0011428-T01-IM5', 'P-0011152-T01-IM5', 'P-0009359-T01-IM5', 'P-0007851-T01-IM5', 'P-0008395-T01-IM5', 'P-0008542-T01-IM5', 'P-0006005-T01-IM5', 'P-0005397-T01-IM5', 'P-0008319-T01-IM5', 'P-0007143-T01-IM5', 'P-0009539-T01-IM5', 'P-0010658-T01-IM5', 'P-0010200-T01-IM5', 'P-0005081-T01-IM5', 'P-0007853-T01-IM5', 'P-0000401-T01-IM3', 'P-0011289-T01-IM5', 'P-0010389-T01-IM5', 'P-0009610-T01-IM5', 'P-0003974-T01-IM3', 'P-0010127-T01-IM5', 'P-0002017-T01-IM3', 'P-0006514-T01-IM5', 'P-0000504-T01-IM3', 'P-0002182-T01-IM3', 'P-0010721-T01-IM5', 'P-0002408-T02-IM5', 'P-0006746-T01-IM5', 'P-0007351-T01-IM5', 'P-0001880-T01-IM3', 'P-0003066-T01-IM3', 'P-0008832-T01-IM5', 'P-0009597-T01-IM5', 'P-0007652-T01-IM5', 'P-0012039-T01-IM5', 'P-0004218-T01-IM5'}\n",
"[WARNING] 2. Warning: Some sample labels in test/clin.csv are missing in test/mut.csv: {'P-0001390-T01-IM3', 'P-0001834-T01-IM3', 'P-0006579-T01-IM5', 'P-0004700-T01-IM5', 'P-0005759-T01-IM5', 'P-0004001-T01-IM3', 'P-0002772-T01-IM3', 'P-0009853-T02-IM5', 'P-0008537-T01-IM5', 'P-0011336-T01-IM5', 'P-0005519-T01-IM5', 'P-0011587-T01-IM5', 'P-0005437-T01-IM5', 'P-0010724-T01-IM5', 'P-0009300-T01-IM5', 'P-0001187-T01-IM3', 'P-0010674-T01-IM5', 'P-0009097-T01-IM5', 'P-0009006-T01-IM5', 'P-0009120-T01-IM5', 'P-0006689-T01-IM5', 'P-0008960-T01-IM5', 'P-0002797-T01-IM3', 'P-0005329-T01-IM5', 'P-0002148-T01-IM3', 'P-0000603-T01-IM3', 'P-0004634-T01-IM5', 'P-0008581-T01-IM5', 'P-0001745-T02-IM5', 'P-0009536-T01-IM5', 'P-0006425-T01-IM5', 'P-0007125-T01-IM5', 'P-0009743-T01-IM5', 'P-0008393-T01-IM5', 'P-0006945-T01-IM5', 'P-0008147-T01-IM5', 'P-0000375-T02-IM5', 'P-0005693-T01-IM5', 'P-0007527-T01-IM5', 'P-0000474-T01-IM3', 'P-0008950-T01-IM5', 'P-0000585-T01-IM3', 'P-0005375-T01-IM5', 'P-0001355-T01-IM3', 'P-0003026-T01-IM3', 'P-0003689-T01-IM5', 'P-0002266-T01-IM3', 'P-0000837-T01-IM3', 'P-0004151-T01-IM5', 'P-0003317-T01-IM5', 'P-0006958-T01-IM5', 'P-0008044-T01-IM5', 'P-0008431-T01-IM5', 'P-0003583-T01-IM5', 'P-0006498-T01-IM5', 'P-0001956-T01-IM3', 'P-0004283-T01-IM5', 'P-0007286-T01-IM5', 'P-0011472-T01-IM5', 'P-0001925-T01-IM3', 'P-0006226-T01-IM5', 'P-0002333-T01-IM3', 'P-0005324-T01-IM5', 'P-0008955-T03-IM5', 'P-0001221-T01-IM3', 'P-0002853-T01-IM3', 'P-0007409-T01-IM5', 'P-0010870-T01-IM5', 'P-0001639-T01-IM3', 'P-0010021-T01-IM5', 'P-0011031-T01-IM5', 'P-0000250-T01-IM3', 'P-0001228-T01-IM3', 'P-0012322-T01-IM5', 'P-0005494-T01-IM5', 'P-0011092-T01-IM5', 'P-0006874-T01-IM5', 'P-0001191-T01-IM3', 'P-0012337-T01-IM5'}\n",
"\n",
"[INFO] ----------------- Processing Data (train) ----------------- \n",
"\n",
"[INFO] ----------------- Cleaning Up Data ----------------- \n",
"\n",
"[INFO] working on layer: mut\n",
"[INFO] Number of NA values: 0\n",
"[INFO] DataFrame mut - Removed 42 features.\n",
"\n",
"[INFO] working on layer: cna\n",
"[INFO] Number of NA values: 0\n",
"[INFO] DataFrame cna - Removed 42 features.\n",
"[INFO] DataFrame mut - Removed 1871 samples (47.75%).\n",
"[INFO] DataFrame cna - Removed 2021 samples (48.79%).\n",
"[INFO] Implementing feature selection using laplacian score for layer: mut with 372 features and 2047 samples \n",
"[INFO] No feature selection applied. Returning original matrix. Demanded # of features is larger than existing number of features\n",
"[INFO] Implementing feature selection using laplacian score for layer: cna with 368 features and 2047 samples \n",
"[INFO] No feature selection applied. Returning original matrix. Demanded # of features is larger than existing number of features\n",
"\n",
"[INFO] ----------------- Processing Data (test) ----------------- \n",
"\n",
"[INFO] ----------------- Cleaning Up Data ----------------- \n",
"\n",
"[INFO] working on layer: mut\n",
"[INFO] Number of NA values: 0\n",
"[INFO] DataFrame mut - Removed 45 features.\n",
"\n",
"[INFO] working on layer: cna\n",
"[INFO] Number of NA values: 0\n",
"[INFO] DataFrame cna - Removed 41 features.\n",
"[INFO] DataFrame mut - Removed 879 samples (51.83%).\n",
"[INFO] DataFrame cna - Removed 935 samples (52.68%).\n",
"\n",
"[INFO] ----------------- Harmonizing Data Sets ----------------- \n",
"\n",
"[INFO] ----------------- Finished Harmonizing ----------------- \n",
"\n",
"[INFO] ----------------- Normalizing Data ----------------- \n",
"\n",
"[INFO] ----------------- Normalizing Data ----------------- \n",
"[INFO] Training Data Stats: {'feature_count in: mut': 361, 'feature_count in: cna': 338, 'sample_count': 2047}\n",
"[INFO] Test Data Stats: {'feature_count in: mut': 361, 'feature_count in: cna': 338, 'sample_count': 817}\n",
"[INFO] Merging Feature Logs...\n",
"[INFO] Data import successful.\n"
]
}
],
"source": [
"data_importer = flexynesis.DataImporter(path ='msk_impact/', \n",
" data_types = ['mut', 'cna'], \n",
" concatenate=False, top_percentile=90, variance_threshold=0.1,\n",
" min_features=500)\n",
"train_dataset, test_dataset = data_importer.import_data()"
]
},
{
"cell_type": "code",
"execution_count": 40,
"id": "1b02ca91-62a1-4f64-8060-fa428844bdff",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'DNA_INPUT': tensor([250., 200., 250., ..., 250., 250., 250.], dtype=torch.float64),\n",
" 'SAMPLE_COVERAGE': tensor([629., 985., 986., ..., 721., 922., 894.], dtype=torch.float64),\n",
" 'TUMOR_PURITY': tensor([90., 70., 50., ..., 60., 80., 60.], dtype=torch.float64),\n",
" 'TMB_NONSYNONYMOUS': tensor([36.2126, 12.2007, 2.9362, ..., 47.9573, 1.9574, 2.9362],\n",
" dtype=torch.float64),\n",
" 'SAMPLE_ID.1': tensor([ 678., 41., 1992., ..., 1945., 1977., 1534.], dtype=torch.float64),\n",
" 'SAMPLE_COLLECTION_SOURCE': tensor([0., 0., 1., ..., 0., 0., 0.], dtype=torch.float64),\n",
" 'SPECIMEN_PRESERVATION_TYPE': tensor([2., 2., 2., ..., 2., 2., 2.], dtype=torch.float64),\n",
" 'SPECIMEN_TYPE': tensor([0., 0., 0., ..., 1., 0., 2.], dtype=torch.float64),\n",
" 'MATCHED_STATUS': tensor([0., 0., 0., ..., 0., 0., 0.], dtype=torch.float64),\n",
" 'SAMPLE_TYPE': tensor([1., 0., 1., ..., 0., 1., 0.], dtype=torch.float64),\n",
" 'PRIMARY_SITE': tensor([4., 2., 6., ..., 4., 1., 4.], dtype=torch.float64),\n",
" 'METASTATIC_SITE': tensor([30., 29., 30., ..., 24., 30., 10.], dtype=torch.float64),\n",
" 'SAMPLE_CLASS': tensor([0., 0., 0., ..., 0., 0., 0.], dtype=torch.float64),\n",
" 'ONCOTREE_CODE': tensor([43., 38., 67., ..., 58., 31., 43.], dtype=torch.float64),\n",
" 'CANCER_TYPE': tensor([15., 3., 18., ..., 15., 9., 15.], dtype=torch.float64),\n",
" 'CANCER_TYPE_DETAILED': tensor([44., 19., 67., ..., 66., 33., 44.], dtype=torch.float64),\n",
" 'SOMATIC_STATUS': tensor([0., 0., 0., ..., 0., 0., 0.], dtype=torch.float64)}"
]
},
"execution_count": 40,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"train_dataset.ann"
]
},
{
"cell_type": "code",
"execution_count": 41,
"id": "014b1006-3c2e-4afa-8c67-6f36a34ebf68",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(array([0., 1., 2., 3., 4., 5., 6., 7., 8.]),\n",
" array([128, 259, 574, 39, 546, 108, 200, 94, 99]))"
]
},
"execution_count": 41,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"np.unique(train_dataset.ann['PRIMARY_SITE'], return_counts=True)"
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "2d31ee94-26b3-4f5f-8642-41769fc4bbfd",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{0: 'Bladder',\n",
" 1: 'Brain',\n",
" 2: 'Breast',\n",
" 3: 'Kidney',\n",
" 4: 'Lung',\n",
" 5: 'Pancreas',\n",
" 6: 'Prostate',\n",
" 7: 'Skin',\n",
" 8: 'Uterus'}"
]
},
"execution_count": 42,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"train_dataset.label_mappings['PRIMARY_SITE']"
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "9290e957-88a4-4df9-a87c-49c698b59713",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Summary for variable: DNA_INPUT\n",
"Numerical Variable Summary: Median = 250.0, Mean = 235.27487835857352\n",
"------\n",
"Summary for variable: SAMPLE_COVERAGE\n",
"Numerical Variable Summary: Median = 735.0, Mean = 731.0004885197851\n",
"------\n",
"Summary for variable: TUMOR_PURITY\n",
"Numerical Variable Summary: Median = 50.0, Mean = 50.638646847770374\n",
"------\n",
"Summary for variable: TMB_NONSYNONYMOUS\n",
"Numerical Variable Summary: Median = 4.436621202, Mean = 7.507028410360039\n",
"------\n",
"Summary for variable: SAMPLE_ID.1\n",
"Categorical Variable Summary:\n",
" Label: P-0000004-T01-IM3, Count: 1\n",
" Label: P-0000030-T01-IM3, Count: 1\n",
" Label: P-0000034-T01-IM3, Count: 1\n",
" Label: P-0000056-T01-IM3, Count: 1\n",
" Label: P-0000058-T01-IM3, Count: 1\n",
" Label: P-0000063-T01-IM3, Count: 1\n",
" Label: P-0000064-T02-IM3, Count: 1\n",
" Label: P-0000066-T01-IM3, Count: 1\n",
" Label: P-0000068-T01-IM3, Count: 1\n",
" Label: P-0000071-T01-IM3, Count: 1\n",
" Label: P-0000075-T01-IM3, Count: 1\n",
" Label: P-0000077-T01-IM3, Count: 1\n",
" Label: P-0000079-T01-IM3, Count: 1\n",
" Label: P-0000080-T01-IM3, Count: 1\n",
" Label: P-0000084-T01-IM3, Count: 1\n",
" Label: P-0000092-T01-IM3, Count: 1\n",
" Label: P-0000093-T01-IM3, Count: 1\n",
" Label: P-0000104-T01-IM3, Count: 1\n",
" Label: P-0000106-T01-IM3, Count: 1\n",
" Label: P-0000110-T01-IM3, Count: 1\n",
" Label: P-0000113-T01-IM3, Count: 1\n",
" Label: P-0000120-T01-IM3, Count: 1\n",
" Label: P-0000122-T01-IM3, Count: 1\n",
" Label: P-0000126-T01-IM3, Count: 1\n",
" Label: P-0000129-T01-IM3, Count: 1\n",
" Label: P-0000130-T01-IM3, Count: 1\n",
" Label: P-0000131-T01-IM3, Count: 1\n",
" Label: P-0000132-T01-IM3, Count: 1\n",
" Label: P-0000140-T01-IM3, Count: 1\n",
" Label: P-0000142-T01-IM3, Count: 1\n",
" Label: P-0000149-T01-IM3, Count: 1\n",
" Label: P-0000156-T01-IM3, Count: 1\n",
" Label: P-0000158-T01-IM3, Count: 1\n",
" Label: P-0000163-T02-IM3, Count: 1\n",
" Label: P-0000165-T01-IM3, Count: 1\n",
" Label: P-0000167-T02-IM3, Count: 1\n",
" Label: P-0000183-T01-IM3, Count: 1\n",
" Label: P-0000187-T01-IM3, Count: 1\n",
" Label: P-0000190-T01-IM3, Count: 1\n",
" Label: P-0000191-T01-IM3, Count: 1\n",
" Label: P-0000195-T01-IM3, Count: 1\n",
" Label: P-0000201-T01-IM3, Count: 1\n",
" Label: P-0000204-T01-IM3, Count: 1\n",
" Label: P-0000205-T01-IM3, Count: 1\n",
" Label: P-0000209-T02-IM3, Count: 1\n",
" Label: P-0000215-T01-IM3, Count: 1\n",
" Label: P-0000220-T01-IM3, Count: 1\n",
" Label: P-0000223-T01-IM3, Count: 1\n",
" Label: P-0000235-T01-IM3, Count: 1\n",
" Label: P-0000242-T01-IM3, Count: 1\n",
" Label: P-0000244-T01-IM3, Count: 1\n",
" Label: P-0000247-T02-IM5, Count: 1\n",
" Label: P-0000252-T01-IM3, Count: 1\n",
" Label: P-0000270-T01-IM3, Count: 1\n",
" Label: P-0000271-T01-IM3, Count: 1\n",
" Label: P-0000274-T01-IM3, Count: 1\n",
" Label: P-0000290-T01-IM3, Count: 1\n",
" Label: P-0000292-T01-IM3, Count: 1\n",
" Label: P-0000308-T01-IM3, Count: 1\n",
" Label: P-0000316-T01-IM3, Count: 1\n",
" Label: P-0000317-T01-IM3, Count: 1\n",
" Label: P-0000318-T01-IM3, Count: 1\n",
" Label: P-0000323-T01-IM3, Count: 1\n",
" Label: P-0000329-T01-IM3, Count: 1\n",
" Label: P-0000335-T02-IM3, Count: 1\n",
" Label: P-0000337-T01-IM3, Count: 1\n",
" Label: P-0000341-T01-IM3, Count: 1\n",
" Label: P-0000345-T01-IM3, Count: 1\n",
" Label: P-0000347-T01-IM3, Count: 1\n",
" Label: P-0000348-T01-IM3, Count: 1\n",
" Label: P-0000353-T01-IM3, Count: 1\n",
" Label: P-0000355-T01-IM3, Count: 1\n",
" Label: P-0000356-T01-IM3, Count: 1\n",
" Label: P-0000363-T01-IM3, Count: 1\n",
" Label: P-0000370-T01-IM3, Count: 1\n",
" Label: P-0000373-T02-IM5, Count: 1\n",
" Label: P-0000378-T01-IM3, Count: 1\n",
" Label: P-0000382-T01-IM3, Count: 1\n",
" Label: P-0000386-T02-IM5, Count: 1\n",
" Label: P-0000390-T01-IM3, Count: 1\n",
" Label: P-0000392-T01-IM3, Count: 1\n",
" Label: P-0000395-T01-IM3, Count: 1\n",
" Label: P-0000399-T01-IM3, Count: 1\n",
" Label: P-0000407-T01-IM3, Count: 1\n",
" Label: P-0000409-T01-IM3, Count: 1\n",
" Label: P-0000410-T01-IM3, Count: 1\n",
" Label: P-0000422-T02-IM3, Count: 1\n",
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" Label: P-0011003-T01-IM5, Count: 1\n",
" Label: P-0011008-T01-IM5, Count: 1\n",
" Label: P-0011010-T01-IM5, Count: 1\n",
" Label: P-0011016-T01-IM5, Count: 1\n",
" Label: P-0011026-T01-IM5, Count: 1\n",
" Label: P-0011030-T01-IM5, Count: 1\n",
" Label: P-0011033-T01-IM5, Count: 1\n",
" Label: P-0011036-T01-IM5, Count: 1\n",
" Label: P-0011038-T01-IM5, Count: 1\n",
" Label: P-0011043-T01-IM5, Count: 1\n",
" Label: P-0011044-T01-IM5, Count: 1\n",
" Label: P-0011072-T01-IM5, Count: 1\n",
" Label: P-0011080-T01-IM5, Count: 1\n",
" Label: P-0011081-T01-IM5, Count: 1\n",
" Label: P-0011090-T01-IM5, Count: 1\n",
" Label: P-0011093-T01-IM5, Count: 1\n",
" Label: P-0011101-T01-IM5, Count: 1\n",
" Label: P-0011119-T01-IM5, Count: 1\n",
" Label: P-0011125-T01-IM5, Count: 1\n",
" Label: P-0011129-T01-IM5, Count: 1\n",
" Label: P-0011136-T01-IM5, Count: 1\n",
" Label: P-0011141-T01-IM5, Count: 1\n",
" Label: P-0011147-T01-IM5, Count: 1\n",
" Label: P-0011154-T01-IM5, Count: 1\n",
" Label: P-0011155-T01-IM5, Count: 1\n",
" Label: P-0011161-T01-IM5, Count: 1\n",
" Label: P-0011181-T01-IM5, Count: 1\n",
" Label: P-0011185-T01-IM5, Count: 1\n",
" Label: P-0011187-T01-IM5, Count: 1\n",
" Label: P-0011192-T01-IM5, Count: 1\n",
" Label: P-0011193-T01-IM5, Count: 1\n",
" Label: P-0011197-T01-IM5, Count: 1\n",
" Label: P-0011201-T01-IM5, Count: 1\n",
" Label: P-0011206-T01-IM5, Count: 1\n",
" Label: P-0011207-T01-IM5, Count: 1\n",
" Label: P-0011210-T01-IM5, Count: 1\n",
" Label: P-0011213-T01-IM5, Count: 1\n",
" Label: P-0011219-T01-IM5, Count: 1\n",
" Label: P-0011237-T01-IM5, Count: 1\n",
" Label: P-0011241-T01-IM5, Count: 1\n",
" Label: P-0011247-T01-IM5, Count: 1\n",
" Label: P-0011257-T01-IM5, Count: 1\n",
" Label: P-0011260-T01-IM5, Count: 1\n",
" Label: P-0011279-T01-IM5, Count: 1\n",
" Label: P-0011285-T01-IM5, Count: 1\n",
" Label: P-0011290-T01-IM5, Count: 1\n",
" Label: P-0011293-T01-IM5, Count: 1\n",
" Label: P-0011297-T01-IM5, Count: 1\n",
" Label: P-0011299-T01-IM5, Count: 1\n",
" Label: P-0011303-T01-IM5, Count: 1\n",
" Label: P-0011308-T01-IM5, Count: 1\n",
" Label: P-0011321-T01-IM5, Count: 1\n",
" Label: P-0011331-T01-IM5, Count: 1\n",
" Label: P-0011334-T01-IM5, Count: 1\n",
" Label: P-0011338-T01-IM5, Count: 1\n",
" Label: P-0011339-T01-IM5, Count: 1\n",
" Label: P-0011344-T01-IM5, Count: 1\n",
" Label: P-0011348-T01-IM5, Count: 1\n",
" Label: P-0011351-T01-IM5, Count: 1\n",
" Label: P-0011361-T01-IM5, Count: 1\n",
" Label: P-0011365-T01-IM5, Count: 1\n",
" Label: P-0011367-T01-IM5, Count: 1\n",
" Label: P-0011370-T01-IM5, Count: 1\n",
" Label: P-0011373-T01-IM5, Count: 1\n",
" Label: P-0011377-T01-IM5, Count: 1\n",
" Label: P-0011378-T01-IM5, Count: 1\n",
" Label: P-0011383-T01-IM5, Count: 1\n",
" Label: P-0011388-T01-IM5, Count: 1\n",
" Label: P-0011389-T01-IM5, Count: 1\n",
" Label: P-0011390-T01-IM5, Count: 1\n",
" Label: P-0011398-T01-IM5, Count: 1\n",
" Label: P-0011401-T01-IM5, Count: 1\n",
" Label: P-0011413-T01-IM5, Count: 1\n",
" Label: P-0011433-T01-IM5, Count: 1\n",
" Label: P-0011434-T01-IM5, Count: 1\n",
" Label: P-0011435-T01-IM5, Count: 1\n",
" Label: P-0011439-T01-IM5, Count: 1\n",
" Label: P-0011442-T01-IM5, Count: 1\n",
" Label: P-0011449-T01-IM5, Count: 1\n",
" Label: P-0011463-T01-IM5, Count: 1\n",
" Label: P-0011464-T01-IM5, Count: 1\n",
" Label: P-0011470-T01-IM5, Count: 1\n",
" Label: P-0011476-T01-IM5, Count: 1\n",
" Label: P-0011483-T01-IM5, Count: 1\n",
" Label: P-0011486-T01-IM5, Count: 1\n",
" Label: P-0011503-T01-IM5, Count: 1\n",
" Label: P-0011505-T01-IM5, Count: 1\n",
" Label: P-0011521-T01-IM5, Count: 1\n",
" Label: P-0011524-T01-IM5, Count: 1\n",
" Label: P-0011535-T01-IM5, Count: 1\n",
" Label: P-0011537-T01-IM5, Count: 1\n",
" Label: P-0011542-T01-IM5, Count: 1\n",
" Label: P-0011544-T01-IM5, Count: 1\n",
" Label: P-0011555-T01-IM5, Count: 1\n",
" Label: P-0011568-T01-IM5, Count: 1\n",
" Label: P-0011580-T01-IM5, Count: 1\n",
" Label: P-0011582-T01-IM5, Count: 1\n",
" Label: P-0011592-T01-IM5, Count: 1\n",
" Label: P-0011594-T01-IM5, Count: 1\n",
" Label: P-0012002-T01-IM5, Count: 1\n",
" Label: P-0012025-T01-IM5, Count: 1\n",
" Label: P-0012027-T01-IM5, Count: 1\n",
" Label: P-0012031-T01-IM5, Count: 1\n",
" Label: P-0012046-T01-IM5, Count: 1\n",
" Label: P-0012048-T01-IM5, Count: 1\n",
" Label: P-0012055-T01-IM5, Count: 1\n",
" Label: P-0012056-T01-IM5, Count: 1\n",
" Label: P-0012070-T01-IM5, Count: 1\n",
" Label: P-0012076-T01-IM5, Count: 1\n",
" Label: P-0012077-T01-IM5, Count: 1\n",
" Label: P-0012080-T01-IM5, Count: 1\n",
" Label: P-0012081-T01-IM5, Count: 1\n",
" Label: P-0012082-T01-IM5, Count: 1\n",
" Label: P-0012084-T01-IM5, Count: 1\n",
" Label: P-0012086-T01-IM5, Count: 1\n",
" Label: P-0012088-T01-IM5, Count: 1\n",
" Label: P-0012091-T01-IM5, Count: 1\n",
" Label: P-0012092-T01-IM5, Count: 1\n",
" Label: P-0012102-T01-IM5, Count: 1\n",
" Label: P-0012109-T01-IM5, Count: 1\n",
" Label: P-0012112-T01-IM5, Count: 1\n",
" Label: P-0012117-T01-IM5, Count: 1\n",
" Label: P-0012127-T01-IM5, Count: 1\n",
" Label: P-0012148-T01-IM5, Count: 1\n",
" Label: P-0012149-T01-IM5, Count: 1\n",
" Label: P-0012153-T01-IM5, Count: 1\n",
" Label: P-0012160-T01-IM5, Count: 1\n",
" Label: P-0012184-T01-IM5, Count: 1\n",
" Label: P-0012186-T01-IM5, Count: 1\n",
" Label: P-0012194-T01-IM5, Count: 1\n",
" Label: P-0012197-T01-IM5, Count: 1\n",
" Label: P-0012199-T01-IM5, Count: 1\n",
" Label: P-0012206-T01-IM5, Count: 1\n",
" Label: P-0012222-T01-IM5, Count: 1\n",
" Label: P-0012241-T01-IM5, Count: 1\n",
" Label: P-0012243-T01-IM5, Count: 1\n",
" Label: P-0012244-T01-IM5, Count: 1\n",
" Label: P-0012250-T01-IM5, Count: 1\n",
" Label: P-0012252-T01-IM5, Count: 1\n",
" Label: P-0012254-T01-IM5, Count: 1\n",
" Label: P-0012258-T01-IM5, Count: 1\n",
" Label: P-0012259-T01-IM5, Count: 1\n",
" Label: P-0012290-T01-IM5, Count: 1\n",
" Label: P-0012303-T01-IM5, Count: 1\n",
" Label: P-0012306-T01-IM5, Count: 1\n",
" Label: P-0012307-T01-IM5, Count: 1\n",
" Label: P-0012312-T01-IM5, Count: 1\n",
" Label: P-0012314-T01-IM5, Count: 1\n",
" Label: P-0012320-T01-IM5, Count: 1\n",
" Label: P-0012329-T01-IM5, Count: 1\n",
" Label: P-0012341-T01-IM5, Count: 1\n",
" Label: P-0012393-T01-IM5, Count: 1\n",
" Label: P-0012395-T01-IM5, Count: 1\n",
" Label: P-0012400-T01-IM5, Count: 1\n",
" Label: P-0012404-T01-IM5, Count: 1\n",
"------\n",
"Summary for variable: SAMPLE_COLLECTION_SOURCE\n",
"Categorical Variable Summary:\n",
" Label: In-House, Count: 1348\n",
" Label: Outside, Count: 699\n",
"------\n",
"Summary for variable: SPECIMEN_PRESERVATION_TYPE\n",
"Categorical Variable Summary:\n",
" Label: Cell Pellet, Count: 4\n",
" Label: DNA, Count: 364\n",
" Label: FFPE, Count: 1679\n",
"------\n",
"Summary for variable: SPECIMEN_TYPE\n",
"Categorical Variable Summary:\n",
" Label: Biopsy, Count: 1126\n",
" Label: Cytology, Count: 172\n",
" Label: Resection, Count: 749\n",
"------\n",
"Summary for variable: MATCHED_STATUS\n",
"Categorical Variable Summary:\n",
" Label: Matched, Count: 2021\n",
" Label: Unmatched, Count: 26\n",
"------\n",
"Summary for variable: SAMPLE_TYPE\n",
"Categorical Variable Summary:\n",
" Label: Metastasis, Count: 1018\n",
" Label: Primary, Count: 1029\n",
"------\n",
"Summary for variable: PRIMARY_SITE\n",
"Categorical Variable Summary:\n",
" Label: Bladder, Count: 128\n",
" Label: Brain, Count: 259\n",
" Label: Breast, Count: 574\n",
" Label: Kidney, Count: 39\n",
" Label: Lung, Count: 546\n",
" Label: Pancreas, Count: 108\n",
" Label: Prostate, Count: 200\n",
" Label: Skin, Count: 94\n",
" Label: Uterus, Count: 99\n",
"------\n",
"Summary for variable: METASTATIC_SITE\n",
"Categorical Variable Summary:\n",
" Label: Abdomen, Count: 10\n",
" Label: Adrenal, Count: 2\n",
" Label: Adrenal Gland, Count: 13\n",
" Label: Arm, Count: 1\n",
" Label: Axilla, Count: 2\n",
" Label: Bile Duct, Count: 1\n",
" Label: Bladder, Count: 6\n",
" Label: Bladder Neck, Count: 1\n",
" Label: Bone, Count: 108\n",
" Label: Bowel, Count: 1\n",
" Label: Brain, Count: 65\n",
" Label: Breast, Count: 2\n",
" Label: Chest Wall, Count: 30\n",
" Label: Colon, Count: 4\n",
" Label: Duodenum, Count: 1\n",
" Label: Epidural, Count: 4\n",
" Label: Epidural Mass, Count: 1\n",
" Label: Flank, Count: 1\n",
" Label: Foot, Count: 1\n",
" Label: In-transit, Count: 11\n",
" Label: Ipsilateral Breast, Count: 4\n",
" Label: Kidney, Count: 1\n",
" Label: Liver, Count: 216\n",
" Label: Lung, Count: 75\n",
" Label: Lymph Node, Count: 235\n",
" Label: Lymph Node, Non-Regional, Count: 1\n",
" Label: Lymph Node, Regional, Count: 15\n",
" Label: Mediastinum, Count: 5\n",
" Label: Muscle, Count: 1\n",
" Label: Neck, Count: 4\n",
" Label: Not Applicable, Count: 1027\n",
" Label: Not available, Count: 1\n",
" Label: Omentum, Count: 13\n",
" Label: Orbit, Count: 1\n",
" Label: Ovary, Count: 9\n",
" Label: Pancreas, Count: 3\n",
" Label: Paraspinal, Count: 1\n",
" Label: Parasternal Mass, Count: 1\n",
" Label: Paratracheal mass, Count: 1\n",
" Label: Pelvis, Count: 17\n",
" Label: Pericardium, Count: 1\n",
" Label: Peritoneum, Count: 6\n",
" Label: Pleura, Count: 36\n",
" Label: Pleural Fluid, Count: 9\n",
" Label: Prostate, Count: 3\n",
" Label: Pubic bone, Count: 1\n",
" Label: Retroperitoneum, Count: 10\n",
" Label: Rib, Count: 1\n",
" Label: Sacral Mass, Count: 1\n",
" Label: Scalp, Count: 3\n",
" Label: Scapula, Count: 1\n",
" Label: Sigmoid Colon, Count: 1\n",
" Label: Skin, Count: 18\n",
" Label: Small Bowel, Count: 4\n",
" Label: Small bowel, Count: 1\n",
" Label: Soft Tissue, Count: 34\n",
" Label: Spine, Count: 3\n",
" Label: Spleen, Count: 1\n",
" Label: Stomach, Count: 2\n",
" Label: Subcutaneous Tissue, Count: 3\n",
" Label: Supraclavicular Mass, Count: 1\n",
" Label: Testis, Count: 2\n",
" Label: Trachea, Count: 2\n",
" Label: Unknown, Count: 1\n",
" Label: Upper Extremity, Count: 1\n",
" Label: Upper Tract, Count: 1\n",
" Label: Urethra, Count: 1\n",
" Label: Vagina, Count: 2\n",
" Label: liver, Count: 1\n",
"------\n",
"Summary for variable: SAMPLE_CLASS\n",
"Categorical Variable Summary:\n",
" Label: Tumor, Count: 2047\n",
"------\n",
"Summary for variable: ONCOTREE_CODE\n",
"Categorical Variable Summary:\n",
" Label: AASTR, Count: 45\n",
" Label: ACBC, Count: 1\n",
" Label: ACRM, Count: 6\n",
" Label: AECA, Count: 1\n",
" Label: ALUCA, Count: 3\n",
" Label: AMPCA, Count: 1\n",
" Label: ANGS, Count: 6\n",
" Label: AOAST, Count: 4\n",
" Label: AODG, Count: 12\n",
" Label: APXA, Count: 1\n",
" Label: ASTR, Count: 4\n",
" Label: ATM, Count: 2\n",
" Label: BA, Count: 1\n",
" Label: BCC, Count: 3\n",
" Label: BCCA, Count: 1\n",
" Label: BLAD, Count: 3\n",
" Label: BLCA, Count: 118\n",
" Label: BRCA, Count: 30\n",
" Label: BRCANOS, Count: 21\n",
" Label: BRCNOS, Count: 20\n",
" Label: CCRCC, Count: 17\n",
" Label: CDRCC, Count: 1\n",
" Label: CHRCC, Count: 3\n",
" Label: CSCC, Count: 4\n",
" Label: CUP, Count: 2\n",
" Label: DDLS, Count: 1\n",
" Label: DFSP, Count: 1\n",
" Label: DLBCLNOS, Count: 2\n",
" Label: EPM, Count: 1\n",
" Label: ESS, Count: 1\n",
" Label: FL, Count: 1\n",
" Label: GBM, Count: 159\n",
" Label: GSARC, Count: 4\n",
" Label: HGESS, Count: 2\n",
" Label: HGGNOS, Count: 8\n",
" Label: HNSC, Count: 1\n",
" Label: IDC, Count: 415\n",
" Label: IHCH, Count: 1\n",
" Label: ILC, Count: 53\n",
" Label: LCLC, Count: 1\n",
" Label: LGGNOS, Count: 1\n",
" Label: LMS, Count: 2\n",
" Label: LNET, Count: 2\n",
" Label: LUAD, Count: 396\n",
" Label: LUAS, Count: 5\n",
" Label: LUNE, Count: 14\n",
" Label: LUPC, Count: 1\n",
" Label: LUSC, Count: 58\n",
" Label: MBC, Count: 5\n",
" Label: MBL, Count: 1\n",
" Label: MCC, Count: 6\n",
" Label: MDLC, Count: 18\n",
" Label: MNG, Count: 5\n",
" Label: MPT, Count: 6\n",
" Label: MZL, Count: 1\n",
" Label: NBL, Count: 3\n",
" Label: NETNOS, Count: 1\n",
" Label: NSCLC, Count: 4\n",
" Label: NSCLCPD, Count: 10\n",
" Label: ODG, Count: 7\n",
" Label: OUSARC, Count: 2\n",
" Label: PAAC, Count: 5\n",
" Label: PAAD, Count: 82\n",
" Label: PAMPCA, Count: 1\n",
" Label: PANET, Count: 15\n",
" Label: PECOMA, Count: 1\n",
" Label: PEMESO, Count: 1\n",
" Label: PRAD, Count: 189\n",
" Label: PRCC, Count: 7\n",
" Label: PRNE, Count: 7\n",
" Label: PRSCC, Count: 4\n",
" Label: RMS, Count: 1\n",
" Label: SARCL, Count: 2\n",
" Label: SARCNOS, Count: 2\n",
" Label: SCB, Count: 2\n",
" Label: SCBC, Count: 1\n",
" Label: SCLC, Count: 41\n",
" Label: SFT, Count: 2\n",
" Label: SKAC, Count: 1\n",
" Label: SKCM, Count: 68\n",
" Label: SPCC, Count: 1\n",
" Label: SRCBC, Count: 1\n",
" Label: TRCC, Count: 2\n",
" Label: UA, Count: 1\n",
" Label: UAS, Count: 1\n",
" Label: UCCC, Count: 6\n",
" Label: UCP, Count: 1\n",
" Label: UCS, Count: 17\n",
" Label: UCU, Count: 1\n",
" Label: UDDC, Count: 1\n",
" Label: UEC, Count: 8\n",
" Label: ULMS, Count: 27\n",
" Label: UMEC, Count: 6\n",
" Label: UMLMS, Count: 1\n",
" Label: UNEC, Count: 1\n",
" Label: UPECOMA, Count: 5\n",
" Label: URCC, Count: 6\n",
" Label: USC, Count: 16\n",
" Label: USTUMP, Count: 1\n",
" Label: UUC, Count: 1\n",
" Label: UUS, Count: 1\n",
" Label: WT, Count: 1\n",
"------\n",
"Summary for variable: CANCER_TYPE\n",
"Categorical Variable Summary:\n",
" Label: Ampullary Cancer, Count: 1\n",
" Label: Ampullary Carcinoma, Count: 1\n",
" Label: Bladder Cancer, Count: 127\n",
" Label: Breast Cancer, Count: 570\n",
" Label: CNS Cancer, Count: 8\n",
" Label: Cancer of Unknown Primary, Count: 3\n",
" Label: Embryonal Tumor, Count: 1\n",
" Label: Endometrial Cancer, Count: 56\n",
" Label: Germ Cell Tumor, Count: 1\n",
" Label: Glioma, Count: 245\n",
" Label: Head and Neck Cancer, Count: 1\n",
" Label: Hepatobiliary Cancer, Count: 1\n",
" Label: Mature B-Cell Neoplasms, Count: 4\n",
" Label: Melanoma, Count: 74\n",
" Label: Mesothelioma, Count: 1\n",
" Label: Non-Small Cell Lung Cancer, Count: 497\n",
" Label: Pancreatic Cancer, Count: 103\n",
" Label: Peripheral Nervous System, Count: 3\n",
" Label: Prostate Cancer, Count: 200\n",
" Label: Renal Cell Carcinoma, Count: 36\n",
" Label: Skin Cancer, Non-Melanoma, Count: 16\n",
" Label: Small Cell Lung Cancer, Count: 41\n",
" Label: Soft Tissue Sarcoma, Count: 15\n",
" Label: Uterine Sarcoma, Count: 41\n",
" Label: Wilms Tumor, Count: 1\n",
"------\n",
"Summary for variable: CANCER_TYPE_DETAILED\n",
"Categorical Variable Summary:\n",
" Label: Acinar Cell Carcinoma of the Pancreas, Count: 5\n",
" Label: Acral Melanoma, Count: 6\n",
" Label: Adenoid Cystic Breast Cancer, Count: 1\n",
" Label: Ampullary Carcinoma, Count: 1\n",
" Label: Anaplastic Astrocytoma, Count: 45\n",
" Label: Anaplastic Oligoastrocytoma, Count: 4\n",
" Label: Anaplastic Oligodendroglioma, Count: 12\n",
" Label: Anaplastic Pleomorphic Xanthoastrocytoma, Count: 1\n",
" Label: Angiosarcoma, Count: 6\n",
" Label: Astrocytoma, Count: 4\n",
" Label: Atypical Lung Carcinoid, Count: 3\n",
" Label: Atypical Meningioma, Count: 2\n",
" Label: Basal Cell Carcinoma, Count: 3\n",
" Label: Bladder Adenocarcinoma, Count: 3\n",
" Label: Bladder Urothelial Carcinoma, Count: 118\n",
" Label: Breast Angiosarcoma, Count: 1\n",
" Label: Breast Invasive Cancer, NOS, Count: 21\n",
" Label: Breast Invasive Carcinoma, NOS, Count: 20\n",
" Label: Breast Invasive Ductal Carcinoma, Count: 415\n",
" Label: Breast Invasive Lobular Carcinoma, Count: 53\n",
" Label: Breast Mixed Ductal and Lobular Carcinoma, Count: 18\n",
" Label: Cancer of Unknown Primary, Count: 2\n",
" Label: Choriocarcinoma, Count: 1\n",
" Label: Chromophobe Renal Cell Carcinoma, Count: 3\n",
" Label: Collecting Duct Renal Cell Carcinoma, Count: 1\n",
" Label: Cutaneous Melanoma, Count: 68\n",
" Label: Cutaneous Squamous Cell Carcinoma, Count: 4\n",
" Label: Dedifferentiated Liposarcoma, Count: 1\n",
" Label: Dermatofibrosarcoma Protuberans, Count: 1\n",
" Label: Diffuse Large B-Cell Lymphoma, NOS, Count: 2\n",
" Label: Endometrial Stromal Sarcoma, Count: 1\n",
" Label: Ependymoma, Count: 1\n",
" Label: Follicular Lymphoma, Count: 1\n",
" Label: Glioblastoma Multiforme, Count: 159\n",
" Label: Gliosarcoma, Count: 4\n",
" Label: Head and Neck Squamous Cell Carcinoma, Count: 1\n",
" Label: High-Grade Endometrial Stromal Sarcoma, Count: 2\n",
" Label: High-Grade Glioma, NOS, Count: 8\n",
" Label: Intrahepatic Cholangiocarcinoma, Count: 1\n",
" Label: Invasive Breast Carcinoma, Count: 30\n",
" Label: Large Cell Lung Carcinoma, Count: 1\n",
" Label: Large Cell Neuroendocrine Carcinoma, Count: 14\n",
" Label: Leiomyosarcoma, Count: 2\n",
" Label: Low-Grade Glioma, NOS, Count: 1\n",
" Label: Lung Adenocarcinoma, Count: 396\n",
" Label: Lung Adenosquamous Carcinoma, Count: 5\n",
" Label: Lung Neuroendocrine Tumor, Count: 2\n",
" Label: Lung Squamous Cell Carcinoma, Count: 58\n",
" Label: Malignant Phyllodes Tumor of the Breast, Count: 6\n",
" Label: Marginal Zone Lymphoma, Count: 1\n",
" Label: Medulloblastoma, Count: 1\n",
" Label: Meningioma, Count: 5\n",
" Label: Merkel Cell Carcinoma, Count: 6\n",
" Label: Metaplastic Breast Cancer, Count: 5\n",
" Label: Neuroblastoma, Count: 3\n",
" Label: Neuroendocrine Tumor, NOS, Count: 1\n",
" Label: Non-Small Cell Lung Cancer, Count: 4\n",
" Label: Oligodendroglioma, Count: 7\n",
" Label: Pancreatic Adenocarcinoma, Count: 82\n",
" Label: Pancreatic Neuroendocrine Tumor, Count: 15\n",
" Label: Pancreatobiliary Ampullary Carcinoma, Count: 1\n",
" Label: Papillary Renal Cell Carcinoma, Count: 7\n",
" Label: Peritoneal Mesothelioma, Count: 1\n",
" Label: Perivascular Epithelioid Cell Tumor, Count: 1\n",
" Label: Plasmacytoid/Signet Ring Cell Bladder Carcinoma, Count: 1\n",
" Label: Pleomorphic Carcinoma of the Lung, Count: 1\n",
" Label: Poorly Differentiated Non-Small Cell Lung Cancer, Count: 10\n",
" Label: Prostate Adenocarcinoma, Count: 189\n",
" Label: Prostate Neuroendocrine Carcinoma, Count: 7\n",
" Label: Prostate Small Cell Carcinoma, Count: 4\n",
" Label: Renal Clear Cell Carcinoma, Count: 17\n",
" Label: Rhabdomyosarcoma, Count: 1\n",
" Label: Sarcoma, NOS, Count: 2\n",
" Label: Sarcomatoid Carcinoma of the Lung, Count: 2\n",
" Label: Sarcomatoid Carcinoma of the Urinary Bladder, Count: 2\n",
" Label: Skin Adnexal Carcinoma, Count: 1\n",
" Label: Small Cell Bladder Cancer, Count: 1\n",
" Label: Small Cell Lung Cancer, Count: 41\n",
" Label: Solitary Fibrous Tumor/Hemangiopericytoma, Count: 2\n",
" Label: Spindle Cell Carcinoma of the Lung, Count: 1\n",
" Label: Sweat Gland Carcinoma/Apocrine Eccrine Carcinoma, Count: 1\n",
" Label: Translocation-Associated Renal Cell Carcinoma, Count: 2\n",
" Label: Unclassified Renal Cell Carcinoma, Count: 6\n",
" Label: Undifferentiated Carcinoma of the Pancreas, Count: 1\n",
" Label: Undifferentiated Uterine Sarcoma, Count: 1\n",
" Label: Urachal Adenocarcinoma, Count: 1\n",
" Label: Urethral Urothelial Carcinoma, Count: 1\n",
" Label: Uterine Adenosarcoma, Count: 1\n",
" Label: Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor, Count: 17\n",
" Label: Uterine Clear Cell Carcinoma, Count: 6\n",
" Label: Uterine Dedifferentiated Carcinoma, Count: 1\n",
" Label: Uterine Endometrioid Carcinoma, Count: 8\n",
" Label: Uterine Leiomyosarcoma, Count: 27\n",
" Label: Uterine Mixed Endometrial Carcinoma, Count: 6\n",
" Label: Uterine Myxoid Leiomyosarcoma, Count: 1\n",
" Label: Uterine Neuroendocrine Carcinoma, Count: 1\n",
" Label: Uterine Perivascular Epithelioid Cell Tumor, Count: 5\n",
" Label: Uterine Sarcoma, Other, Count: 2\n",
" Label: Uterine Serous Carcinoma/Uterine Papillary Serous Carcinoma, Count: 16\n",
" Label: Uterine Smooth Muscle Tumor of Uncertain Malignant Potential, Count: 1\n",
" Label: Uterine Undifferentiated Carcinoma, Count: 1\n",
" Label: Wilms' Tumor, Count: 1\n",
"------\n",
"Summary for variable: SOMATIC_STATUS\n",
"Categorical Variable Summary:\n",
" Label: Matched, Count: 2021\n",
" Label: Unmatched, Count: 26\n",
"------\n"
]
}
],
"source": [
"flexynesis.print_summary_stats(train_dataset)"
]
},
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