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| 1 | { |
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| 2 | "cells": [ |
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| 3 | { |
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| 4 | "cell_type": "markdown", |
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| 5 | "metadata": {}, |
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| 6 | "source": [ |
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| 7 | "## Basic API Usage of KGWAS\n", |
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| 8 | "\n", |
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| 9 | "KGWAS consists of two main class `KGWAS` and `KGWAS_Data`. `KGWAS` is the main class for the KGWAS model, and `KGWAS_Data` is the class for the data manipulation. In default, to ensure fast user experience, we provide a default fast mode of KGWAS, which uses Enformer embedding for variant feature and ESM embedding for gene features (instead of the baselineLD for variant and PoPS for gene since they are large files). For the fast mode, you do not need to download any data, the KGWAS API will automatically download the relevant files. This mode can be used to apply KGWAS to your own GWAS sumstats. " |
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| 10 | ] |
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| 11 | }, |
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| 12 | { |
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| 13 | "cell_type": "code", |
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| 14 | "execution_count": 1, |
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| 15 | "metadata": {}, |
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| 16 | "outputs": [ |
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| 17 | { |
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| 18 | "name": "stdout", |
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| 19 | "output_type": "stream", |
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| 20 | "text": [ |
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| 21 | "All required data files are present.\n", |
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| 22 | "--loading KG---\n", |
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| 23 | "--using enformer SNP embedding--\n", |
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| 24 | "--using random go embedding--\n", |
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| 25 | "--using ESM gene embedding--\n" |
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| 26 | ] |
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| 27 | } |
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| 28 | ], |
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| 29 | "source": [ |
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| 30 | "import sys\n", |
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| 31 | "sys.path.append('../')\n", |
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| 32 | "\n", |
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| 33 | "from kgwas import KGWAS, KGWAS_Data\n", |
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| 34 | "data = KGWAS_Data(data_path = './data/')\n", |
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| 35 | "data.load_kg()" |
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| 36 | ] |
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| 37 | }, |
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| 38 | { |
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| 39 | "cell_type": "markdown", |
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| 40 | "metadata": {}, |
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| 41 | "source": [ |
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| 42 | "Now, the data needed for training is downloaded from the server and the knowledge graph is loaded. Next, we load the GWAS file. Here, we are using an example GWAS file, which is also automatically downloaded from the server. But you can also use your own GWAS file. The GWAS file should be in the format of a pandas DataFrame with columns `CHR`/`#CHROM`, `SNP`, `P`, `N`. Note that at the moment, our knowledge graph is UKBioBank directly genotyped variant set so it will automatically takes the overlap with the KG. Current efforts are underway for improving the coverage of the KG." |
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| 43 | ] |
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| 44 | }, |
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| 45 | { |
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| 46 | "cell_type": "code", |
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| 47 | "execution_count": 2, |
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| 48 | "metadata": {}, |
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| 49 | "outputs": [ |
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| 50 | { |
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| 51 | "name": "stdout", |
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| 52 | "output_type": "stream", |
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| 53 | "text": [ |
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| 54 | "Loading example GWAS file...\n", |
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| 55 | "Example file already exists locally.\n", |
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| 56 | "Loading GWAS file from ./data/biochemistry_Creatinine_fastgwa_full_10000_1.fastGWA...\n", |
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| 57 | "Number of SNPs in the KG: 784256\n", |
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| 58 | "Number of SNPs in the GWAS: 542758\n", |
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| 59 | "Number of SNPs in the KG variant set: 542758\n", |
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| 60 | "Using ldsc weight...\n", |
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| 61 | "ldsc_weight mean: 0.9999999999999993\n" |
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| 62 | ] |
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| 63 | } |
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| 64 | ], |
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| 65 | "source": [ |
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| 66 | "data.load_external_gwas(example_file = True)\n", |
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| 67 | "data.process_gwas_file()\n", |
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| 68 | "data.prepare_split()" |
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| 69 | ] |
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| 70 | }, |
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| 71 | { |
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| 72 | "cell_type": "code", |
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| 73 | "execution_count": 3, |
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| 74 | "metadata": {}, |
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| 75 | "outputs": [ |
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| 76 | { |
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| 77 | "data": { |
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| 78 | "text/html": [ |
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| 79 | "<div>\n", |
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| 80 | "<style scoped>\n", |
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| 81 | " .dataframe tbody tr th:only-of-type {\n", |
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| 82 | " vertical-align: middle;\n", |
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| 83 | " }\n", |
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| 84 | "\n", |
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| 85 | " .dataframe tbody tr th {\n", |
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| 86 | " vertical-align: top;\n", |
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| 87 | " }\n", |
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| 88 | "\n", |
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| 89 | " .dataframe thead th {\n", |
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| 90 | " text-align: right;\n", |
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| 91 | " }\n", |
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| 92 | "</style>\n", |
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| 93 | "<table border=\"1\" class=\"dataframe\">\n", |
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| 94 | " <thead>\n", |
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| 95 | " <tr style=\"text-align: right;\">\n", |
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| 96 | " <th></th>\n", |
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| 97 | " <th>#CHROM</th>\n", |
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| 98 | " <th>ID</th>\n", |
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| 99 | " <th>POS</th>\n", |
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| 100 | " <th>A1</th>\n", |
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| 101 | " <th>A2</th>\n", |
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| 102 | " <th>N</th>\n", |
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| 103 | " <th>AF1</th>\n", |
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| 104 | " <th>BETA</th>\n", |
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| 105 | " <th>SE</th>\n", |
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| 106 | " <th>P</th>\n", |
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| 107 | " <th>ld_score</th>\n", |
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| 108 | " <th>w_ld_score</th>\n", |
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| 109 | " <th>y</th>\n", |
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| 110 | " </tr>\n", |
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| 111 | " </thead>\n", |
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| 112 | " <tbody>\n", |
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| 113 | " <tr>\n", |
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| 114 | " <th>0</th>\n", |
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| 115 | " <td>1</td>\n", |
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| 116 | " <td>rs3131962</td>\n", |
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| 117 | " <td>756604</td>\n", |
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| 118 | " <td>A</td>\n", |
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| 119 | " <td>G</td>\n", |
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| 120 | " <td>9988</td>\n", |
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| 121 | " <td>0.131007</td>\n", |
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| 122 | " <td>-0.117134</td>\n", |
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| 123 | " <td>0.246231</td>\n", |
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| 124 | " <td>0.634282</td>\n", |
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| 125 | " <td>72.862240</td>\n", |
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| 126 | " <td>4.474788</td>\n", |
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| 127 | " <td>0.226298</td>\n", |
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| 128 | " </tr>\n", |
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| 129 | " <tr>\n", |
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| 130 | " <th>1</th>\n", |
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| 131 | " <td>1</td>\n", |
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| 132 | " <td>rs12562034</td>\n", |
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| 133 | " <td>768448</td>\n", |
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| 134 | " <td>A</td>\n", |
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| 135 | " <td>G</td>\n", |
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| 136 | " <td>9978</td>\n", |
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| 137 | " <td>0.104981</td>\n", |
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| 138 | " <td>-0.064894</td>\n", |
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| 139 | " <td>0.273746</td>\n", |
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| 140 | " <td>0.812611</td>\n", |
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| 141 | " <td>34.749233</td>\n", |
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| 142 | " <td>1.877341</td>\n", |
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| 143 | " <td>0.056197</td>\n", |
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| 144 | " </tr>\n", |
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| 145 | " <tr>\n", |
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| 146 | " <th>2</th>\n", |
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| 147 | " <td>1</td>\n", |
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| 148 | " <td>rs4040617</td>\n", |
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| 149 | " <td>779322</td>\n", |
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| 150 | " <td>G</td>\n", |
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| 151 | " <td>A</td>\n", |
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| 152 | " <td>9975</td>\n", |
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| 153 | " <td>0.129123</td>\n", |
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| 154 | " <td>-0.001462</td>\n", |
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| 155 | " <td>0.247254</td>\n", |
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| 156 | " <td>0.995281</td>\n", |
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| 157 | " <td>72.271390</td>\n", |
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| 158 | " <td>4.208873</td>\n", |
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| 159 | " <td>0.000035</td>\n", |
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| 160 | " </tr>\n", |
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| 161 | " <tr>\n", |
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| 162 | " <th>3</th>\n", |
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| 163 | " <td>1</td>\n", |
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| 164 | " <td>rs79373928</td>\n", |
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| 165 | " <td>801536</td>\n", |
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| 166 | " <td>G</td>\n", |
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| 167 | " <td>T</td>\n", |
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| 168 | " <td>9994</td>\n", |
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| 169 | " <td>0.014659</td>\n", |
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| 170 | " <td>0.081544</td>\n", |
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| 171 | " <td>0.688261</td>\n", |
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| 172 | " <td>0.905688</td>\n", |
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| 173 | " <td>16.740126</td>\n", |
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| 174 | " <td>1.949177</td>\n", |
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| 175 | " <td>0.014037</td>\n", |
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| 176 | " </tr>\n", |
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| 177 | " <tr>\n", |
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| 178 | " <th>4</th>\n", |
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| 179 | " <td>1</td>\n", |
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| 180 | " <td>rs11240779</td>\n", |
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| 181 | " <td>808631</td>\n", |
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| 182 | " <td>G</td>\n", |
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| 183 | " <td>A</td>\n", |
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| 184 | " <td>9919</td>\n", |
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| 185 | " <td>0.226737</td>\n", |
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| 186 | " <td>-0.184268</td>\n", |
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| 187 | " <td>0.198982</td>\n", |
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| 188 | " <td>0.354418</td>\n", |
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| 189 | " <td>50.215000</td>\n", |
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| 190 | " <td>2.825456</td>\n", |
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| 191 | " <td>0.857575</td>\n", |
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| 192 | " </tr>\n", |
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| 193 | " <tr>\n", |
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| 194 | " <th>...</th>\n", |
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| 195 | " <td>...</td>\n", |
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| 196 | " <td>...</td>\n", |
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| 197 | " <td>...</td>\n", |
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| 198 | " <td>...</td>\n", |
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| 199 | " <td>...</td>\n", |
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| 200 | " <td>...</td>\n", |
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| 201 | " <td>...</td>\n", |
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| 202 | " <td>...</td>\n", |
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| 203 | " <td>...</td>\n", |
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| 204 | " <td>...</td>\n", |
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| 205 | " <td>...</td>\n", |
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| 206 | " <td>...</td>\n", |
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| 207 | " <td>...</td>\n", |
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| 208 | " </tr>\n", |
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| 209 | " <tr>\n", |
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| 210 | " <th>542753</th>\n", |
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| 211 | " <td>22</td>\n", |
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| 212 | " <td>rs73174435</td>\n", |
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| 213 | " <td>51174939</td>\n", |
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| 214 | " <td>T</td>\n", |
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| 215 | " <td>C</td>\n", |
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| 216 | " <td>9979</td>\n", |
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| 217 | " <td>0.056118</td>\n", |
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| 218 | " <td>-0.158762</td>\n", |
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| 219 | " <td>0.362390</td>\n", |
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| 220 | " <td>0.661316</td>\n", |
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| 221 | " <td>21.981667</td>\n", |
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| 222 | " <td>1.363001</td>\n", |
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| 223 | " <td>0.191929</td>\n", |
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| 224 | " </tr>\n", |
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| 225 | " <tr>\n", |
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| 226 | " <th>542754</th>\n", |
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| 227 | " <td>22</td>\n", |
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| 228 | " <td>rs3810648</td>\n", |
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| 229 | " <td>51175626</td>\n", |
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| 230 | " <td>G</td>\n", |
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| 231 | " <td>A</td>\n", |
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| 232 | " <td>9931</td>\n", |
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| 233 | " <td>0.058856</td>\n", |
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| 234 | " <td>0.272493</td>\n", |
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| 235 | " <td>0.352508</td>\n", |
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| 236 | " <td>0.439515</td>\n", |
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| 237 | " <td>34.619377</td>\n", |
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| 238 | " <td>1.804193</td>\n", |
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| 239 | " <td>0.597548</td>\n", |
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| 240 | " </tr>\n", |
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| 241 | " <tr>\n", |
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| 242 | " <th>542755</th>\n", |
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| 243 | " <td>22</td>\n", |
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| 244 | " <td>rs5771002</td>\n", |
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| 245 | " <td>51183255</td>\n", |
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| 246 | " <td>A</td>\n", |
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| 247 | " <td>G</td>\n", |
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| 248 | " <td>9840</td>\n", |
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| 249 | " <td>0.333638</td>\n", |
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| 250 | " <td>0.116325</td>\n", |
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| 251 | " <td>0.175675</td>\n", |
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| 252 | " <td>0.507869</td>\n", |
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| 253 | " <td>16.231083</td>\n", |
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| 254 | " <td>1.273770</td>\n", |
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| 255 | " <td>0.438456</td>\n", |
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| 256 | " </tr>\n", |
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| 257 | " <tr>\n", |
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| 258 | " <th>542756</th>\n", |
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| 259 | " <td>22</td>\n", |
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| 260 | " <td>rs3865764</td>\n", |
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| 261 | " <td>51185848</td>\n", |
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| 262 | " <td>G</td>\n", |
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| 263 | " <td>A</td>\n", |
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| 264 | " <td>9974</td>\n", |
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| 265 | " <td>0.051133</td>\n", |
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| 266 | " <td>-0.026670</td>\n", |
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| 267 | " <td>0.376132</td>\n", |
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| 268 | " <td>0.943472</td>\n", |
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| 269 | " <td>18.649513</td>\n", |
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| 270 | " <td>1.010000</td>\n", |
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| 271 | " <td>0.005028</td>\n", |
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| 272 | " </tr>\n", |
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| 273 | " <tr>\n", |
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| 274 | " <th>542757</th>\n", |
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| 275 | " <td>22</td>\n", |
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| 276 | " <td>rs142680588</td>\n", |
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| 277 | " <td>51193629</td>\n", |
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| 278 | " <td>G</td>\n", |
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| 279 | " <td>A</td>\n", |
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| 280 | " <td>9981</td>\n", |
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| 281 | " <td>0.076595</td>\n", |
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| 282 | " <td>-0.109532</td>\n", |
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| 283 | " <td>0.312971</td>\n", |
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| 284 | " <td>0.726358</td>\n", |
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| 285 | " <td>52.471287</td>\n", |
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| 286 | " <td>1.873861</td>\n", |
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| 287 | " <td>0.122482</td>\n", |
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| 288 | " </tr>\n", |
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| 289 | " </tbody>\n", |
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| 290 | "</table>\n", |
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| 291 | "<p>542758 rows × 13 columns</p>\n", |
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| 292 | "</div>" |
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| 293 | ], |
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| 294 | "text/plain": [ |
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| 295 | " #CHROM ID POS A1 A2 N AF1 BETA \\\n", |
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| 296 | "0 1 rs3131962 756604 A G 9988 0.131007 -0.117134 \n", |
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| 297 | "1 1 rs12562034 768448 A G 9978 0.104981 -0.064894 \n", |
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| 298 | "2 1 rs4040617 779322 G A 9975 0.129123 -0.001462 \n", |
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| 299 | "3 1 rs79373928 801536 G T 9994 0.014659 0.081544 \n", |
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| 300 | "4 1 rs11240779 808631 G A 9919 0.226737 -0.184268 \n", |
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| 301 | "... ... ... ... .. .. ... ... ... \n", |
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| 302 | "542753 22 rs73174435 51174939 T C 9979 0.056118 -0.158762 \n", |
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| 303 | "542754 22 rs3810648 51175626 G A 9931 0.058856 0.272493 \n", |
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| 304 | "542755 22 rs5771002 51183255 A G 9840 0.333638 0.116325 \n", |
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| 305 | "542756 22 rs3865764 51185848 G A 9974 0.051133 -0.026670 \n", |
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| 306 | "542757 22 rs142680588 51193629 G A 9981 0.076595 -0.109532 \n", |
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| 307 | "\n", |
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| 308 | " SE P ld_score w_ld_score y \n", |
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| 309 | "0 0.246231 0.634282 72.862240 4.474788 0.226298 \n", |
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| 310 | "1 0.273746 0.812611 34.749233 1.877341 0.056197 \n", |
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| 311 | "2 0.247254 0.995281 72.271390 4.208873 0.000035 \n", |
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| 312 | "3 0.688261 0.905688 16.740126 1.949177 0.014037 \n", |
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| 313 | "4 0.198982 0.354418 50.215000 2.825456 0.857575 \n", |
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| 314 | "... ... ... ... ... ... \n", |
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| 315 | "542753 0.362390 0.661316 21.981667 1.363001 0.191929 \n", |
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| 316 | "542754 0.352508 0.439515 34.619377 1.804193 0.597548 \n", |
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| 317 | "542755 0.175675 0.507869 16.231083 1.273770 0.438456 \n", |
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| 318 | "542756 0.376132 0.943472 18.649513 1.010000 0.005028 \n", |
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| 319 | "542757 0.312971 0.726358 52.471287 1.873861 0.122482 \n", |
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| 320 | "\n", |
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| 321 | "[542758 rows x 13 columns]" |
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| 322 | ] |
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| 323 | }, |
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| 324 | "execution_count": 3, |
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| 325 | "metadata": {}, |
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| 326 | "output_type": "execute_result" |
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| 327 | } |
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| 328 | ], |
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| 329 | "source": [ |
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| 330 | "data.lr_uni" |
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| 331 | ] |
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| 332 | }, |
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| 333 | { |
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| 334 | "cell_type": "markdown", |
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| 335 | "metadata": {}, |
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| 336 | "source": [ |
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| 337 | "Next, we are ready to train the model! Here we are using epoch = 1 for the demo purpose, but in reality, you should use a higher number of epochs for better performance." |
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| 338 | ] |
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| 339 | }, |
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| 340 | { |
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| 341 | "cell_type": "code", |
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| 342 | "execution_count": 4, |
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| 343 | "metadata": {}, |
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| 344 | "outputs": [ |
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| 345 | { |
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| 346 | "name": "stderr", |
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| 347 | "output_type": "stream", |
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| 348 | "text": [ |
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| 349 | "Creating data loader...\n", |
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| 350 | "Start Training...\n", |
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| 351 | "Training Progress Epoch 1/1: 52%|█████▏ | 500/956 [12:56<15:47, 2.08s/it]Epoch 1 Step 501 Train Loss: 1.8115\n", |
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| 352 | "Training Progress Epoch 1/1: 100%|██████████| 956/956 [24:26<00:00, 1.53s/it]\n", |
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| 353 | "100%|██████████| 50/50 [00:58<00:00, 1.17s/it]\n", |
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| 354 | "Epoch 1: Validation MSE: 2.1730 Validation Pearson: 0.0096. \n", |
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| 355 | "Saving models to ./data//model/test\n", |
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| 356 | "100%|██████████| 54/54 [00:56<00:00, 1.04s/it]\n", |
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| 357 | "100%|██████████| 1061/1061 [05:40<00:00, 3.11it/s]\n" |
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| 358 | ] |
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| 359 | }, |
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| 360 | { |
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| 361 | "name": "stdout", |
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| 362 | "output_type": "stream", |
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| 363 | "text": [ |
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| 364 | "KGWAS prediction and p-values saved to ./data//model_pred/new_experiments/test_pred.csv\n" |
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| 365 | ] |
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| 366 | } |
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| 367 | ], |
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| 368 | "source": [ |
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| 369 | "run = KGWAS(data, device = 'cuda:9', exp_name = 'test')\n", |
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| 370 | "run.initialize_model()\n", |
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| 371 | "run.train(epoch = 1)" |
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| 372 | ] |
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| 373 | }, |
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| 374 | { |
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| 375 | "cell_type": "markdown", |
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| 376 | "metadata": {}, |
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| 377 | "source": [ |
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| 378 | "The output of the model is saved to `/model_pred/new_experiments/{exp_name}_pred.csv`. You can also load it via `run.kgwas_res`. The model is also saved to `/model/{exp_name}`." |
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| 379 | ] |
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| 380 | }, |
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| 381 | { |
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| 382 | "cell_type": "code", |
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| 383 | "execution_count": 5, |
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| 384 | "metadata": {}, |
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| 385 | "outputs": [ |
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| 386 | { |
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| 387 | "data": { |
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| 388 | "text/html": [ |
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| 389 | "<div>\n", |
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| 390 | "<style scoped>\n", |
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| 391 | " .dataframe tbody tr th:only-of-type {\n", |
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| 392 | " vertical-align: middle;\n", |
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| 393 | " }\n", |
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| 394 | "\n", |
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| 395 | " .dataframe tbody tr th {\n", |
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| 396 | " vertical-align: top;\n", |
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| 397 | " }\n", |
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| 398 | "\n", |
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| 399 | " .dataframe thead th {\n", |
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| 400 | " text-align: right;\n", |
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| 401 | " }\n", |
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| 402 | "</style>\n", |
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| 403 | "<table border=\"1\" class=\"dataframe\">\n", |
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| 404 | " <thead>\n", |
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| 405 | " <tr style=\"text-align: right;\">\n", |
||
| 406 | " <th></th>\n", |
||
| 407 | " <th>#CHROM</th>\n", |
||
| 408 | " <th>ID</th>\n", |
||
| 409 | " <th>POS</th>\n", |
||
| 410 | " <th>A1</th>\n", |
||
| 411 | " <th>A2</th>\n", |
||
| 412 | " <th>N</th>\n", |
||
| 413 | " <th>AF1</th>\n", |
||
| 414 | " <th>BETA</th>\n", |
||
| 415 | " <th>SE</th>\n", |
||
| 416 | " <th>P</th>\n", |
||
| 417 | " <th>ld_score</th>\n", |
||
| 418 | " <th>w_ld_score</th>\n", |
||
| 419 | " <th>y</th>\n", |
||
| 420 | " <th>pred</th>\n", |
||
| 421 | " <th>P_weighted</th>\n", |
||
| 422 | " <th>KGWAS_P</th>\n", |
||
| 423 | " </tr>\n", |
||
| 424 | " </thead>\n", |
||
| 425 | " <tbody>\n", |
||
| 426 | " <tr>\n", |
||
| 427 | " <th>0</th>\n", |
||
| 428 | " <td>1</td>\n", |
||
| 429 | " <td>rs3131962</td>\n", |
||
| 430 | " <td>756604</td>\n", |
||
| 431 | " <td>A</td>\n", |
||
| 432 | " <td>G</td>\n", |
||
| 433 | " <td>9988</td>\n", |
||
| 434 | " <td>0.131007</td>\n", |
||
| 435 | " <td>-0.117134</td>\n", |
||
| 436 | " <td>0.246231</td>\n", |
||
| 437 | " <td>0.634282</td>\n", |
||
| 438 | " <td>72.862240</td>\n", |
||
| 439 | " <td>4.474788</td>\n", |
||
| 440 | " <td>0.226298</td>\n", |
||
| 441 | " <td>1.082365</td>\n", |
||
| 442 | " <td>0.234167</td>\n", |
||
| 443 | " <td>0.346428</td>\n", |
||
| 444 | " </tr>\n", |
||
| 445 | " <tr>\n", |
||
| 446 | " <th>1</th>\n", |
||
| 447 | " <td>1</td>\n", |
||
| 448 | " <td>rs12562034</td>\n", |
||
| 449 | " <td>768448</td>\n", |
||
| 450 | " <td>A</td>\n", |
||
| 451 | " <td>G</td>\n", |
||
| 452 | " <td>9978</td>\n", |
||
| 453 | " <td>0.104981</td>\n", |
||
| 454 | " <td>-0.064894</td>\n", |
||
| 455 | " <td>0.273746</td>\n", |
||
| 456 | " <td>0.812611</td>\n", |
||
| 457 | " <td>34.749233</td>\n", |
||
| 458 | " <td>1.877341</td>\n", |
||
| 459 | " <td>0.056197</td>\n", |
||
| 460 | " <td>1.087724</td>\n", |
||
| 461 | " <td>0.382894</td>\n", |
||
| 462 | " <td>0.566456</td>\n", |
||
| 463 | " </tr>\n", |
||
| 464 | " <tr>\n", |
||
| 465 | " <th>2</th>\n", |
||
| 466 | " <td>1</td>\n", |
||
| 467 | " <td>rs4040617</td>\n", |
||
| 468 | " <td>779322</td>\n", |
||
| 469 | " <td>G</td>\n", |
||
| 470 | " <td>A</td>\n", |
||
| 471 | " <td>9975</td>\n", |
||
| 472 | " <td>0.129123</td>\n", |
||
| 473 | " <td>-0.001462</td>\n", |
||
| 474 | " <td>0.247254</td>\n", |
||
| 475 | " <td>0.995281</td>\n", |
||
| 476 | " <td>72.271390</td>\n", |
||
| 477 | " <td>4.208873</td>\n", |
||
| 478 | " <td>0.000035</td>\n", |
||
| 479 | " <td>1.058530</td>\n", |
||
| 480 | " <td>0.995281</td>\n", |
||
| 481 | " <td>1</td>\n", |
||
| 482 | " </tr>\n", |
||
| 483 | " <tr>\n", |
||
| 484 | " <th>3</th>\n", |
||
| 485 | " <td>1</td>\n", |
||
| 486 | " <td>rs79373928</td>\n", |
||
| 487 | " <td>801536</td>\n", |
||
| 488 | " <td>G</td>\n", |
||
| 489 | " <td>T</td>\n", |
||
| 490 | " <td>9994</td>\n", |
||
| 491 | " <td>0.014659</td>\n", |
||
| 492 | " <td>0.081544</td>\n", |
||
| 493 | " <td>0.688261</td>\n", |
||
| 494 | " <td>0.905688</td>\n", |
||
| 495 | " <td>16.740126</td>\n", |
||
| 496 | " <td>1.949177</td>\n", |
||
| 497 | " <td>0.014037</td>\n", |
||
| 498 | " <td>1.105125</td>\n", |
||
| 499 | " <td>0.225107</td>\n", |
||
| 500 | " <td>0.333025</td>\n", |
||
| 501 | " </tr>\n", |
||
| 502 | " <tr>\n", |
||
| 503 | " <th>4</th>\n", |
||
| 504 | " <td>1</td>\n", |
||
| 505 | " <td>rs11240779</td>\n", |
||
| 506 | " <td>808631</td>\n", |
||
| 507 | " <td>G</td>\n", |
||
| 508 | " <td>A</td>\n", |
||
| 509 | " <td>9919</td>\n", |
||
| 510 | " <td>0.226737</td>\n", |
||
| 511 | " <td>-0.184268</td>\n", |
||
| 512 | " <td>0.198982</td>\n", |
||
| 513 | " <td>0.354418</td>\n", |
||
| 514 | " <td>50.215000</td>\n", |
||
| 515 | " <td>2.825456</td>\n", |
||
| 516 | " <td>0.857575</td>\n", |
||
| 517 | " <td>1.081468</td>\n", |
||
| 518 | " <td>0.041646</td>\n", |
||
| 519 | " <td>0.061612</td>\n", |
||
| 520 | " </tr>\n", |
||
| 521 | " <tr>\n", |
||
| 522 | " <th>...</th>\n", |
||
| 523 | " <td>...</td>\n", |
||
| 524 | " <td>...</td>\n", |
||
| 525 | " <td>...</td>\n", |
||
| 526 | " <td>...</td>\n", |
||
| 527 | " <td>...</td>\n", |
||
| 528 | " <td>...</td>\n", |
||
| 529 | " <td>...</td>\n", |
||
| 530 | " <td>...</td>\n", |
||
| 531 | " <td>...</td>\n", |
||
| 532 | " <td>...</td>\n", |
||
| 533 | " <td>...</td>\n", |
||
| 534 | " <td>...</td>\n", |
||
| 535 | " <td>...</td>\n", |
||
| 536 | " <td>...</td>\n", |
||
| 537 | " <td>...</td>\n", |
||
| 538 | " <td>...</td>\n", |
||
| 539 | " </tr>\n", |
||
| 540 | " <tr>\n", |
||
| 541 | " <th>542753</th>\n", |
||
| 542 | " <td>22</td>\n", |
||
| 543 | " <td>rs73174435</td>\n", |
||
| 544 | " <td>51174939</td>\n", |
||
| 545 | " <td>T</td>\n", |
||
| 546 | " <td>C</td>\n", |
||
| 547 | " <td>9979</td>\n", |
||
| 548 | " <td>0.056118</td>\n", |
||
| 549 | " <td>-0.158762</td>\n", |
||
| 550 | " <td>0.362390</td>\n", |
||
| 551 | " <td>0.661316</td>\n", |
||
| 552 | " <td>21.981667</td>\n", |
||
| 553 | " <td>1.363001</td>\n", |
||
| 554 | " <td>0.191929</td>\n", |
||
| 555 | " <td>1.008835</td>\n", |
||
| 556 | " <td>0.233609</td>\n", |
||
| 557 | " <td>0.345602</td>\n", |
||
| 558 | " </tr>\n", |
||
| 559 | " <tr>\n", |
||
| 560 | " <th>542754</th>\n", |
||
| 561 | " <td>22</td>\n", |
||
| 562 | " <td>rs3810648</td>\n", |
||
| 563 | " <td>51175626</td>\n", |
||
| 564 | " <td>G</td>\n", |
||
| 565 | " <td>A</td>\n", |
||
| 566 | " <td>9931</td>\n", |
||
| 567 | " <td>0.058856</td>\n", |
||
| 568 | " <td>0.272493</td>\n", |
||
| 569 | " <td>0.352508</td>\n", |
||
| 570 | " <td>0.439515</td>\n", |
||
| 571 | " <td>34.619377</td>\n", |
||
| 572 | " <td>1.804193</td>\n", |
||
| 573 | " <td>0.597548</td>\n", |
||
| 574 | " <td>1.034187</td>\n", |
||
| 575 | " <td>0.439515</td>\n", |
||
| 576 | " <td>0.650221</td>\n", |
||
| 577 | " </tr>\n", |
||
| 578 | " <tr>\n", |
||
| 579 | " <th>542755</th>\n", |
||
| 580 | " <td>22</td>\n", |
||
| 581 | " <td>rs5771002</td>\n", |
||
| 582 | " <td>51183255</td>\n", |
||
| 583 | " <td>A</td>\n", |
||
| 584 | " <td>G</td>\n", |
||
| 585 | " <td>9840</td>\n", |
||
| 586 | " <td>0.333638</td>\n", |
||
| 587 | " <td>0.116325</td>\n", |
||
| 588 | " <td>0.175675</td>\n", |
||
| 589 | " <td>0.507869</td>\n", |
||
| 590 | " <td>16.231083</td>\n", |
||
| 591 | " <td>1.273770</td>\n", |
||
| 592 | " <td>0.438456</td>\n", |
||
| 593 | " <td>1.093221</td>\n", |
||
| 594 | " <td>0.449038</td>\n", |
||
| 595 | " <td>0.66431</td>\n", |
||
| 596 | " </tr>\n", |
||
| 597 | " <tr>\n", |
||
| 598 | " <th>542756</th>\n", |
||
| 599 | " <td>22</td>\n", |
||
| 600 | " <td>rs3865764</td>\n", |
||
| 601 | " <td>51185848</td>\n", |
||
| 602 | " <td>G</td>\n", |
||
| 603 | " <td>A</td>\n", |
||
| 604 | " <td>9974</td>\n", |
||
| 605 | " <td>0.051133</td>\n", |
||
| 606 | " <td>-0.026670</td>\n", |
||
| 607 | " <td>0.376132</td>\n", |
||
| 608 | " <td>0.943472</td>\n", |
||
| 609 | " <td>18.649513</td>\n", |
||
| 610 | " <td>1.010000</td>\n", |
||
| 611 | " <td>0.005028</td>\n", |
||
| 612 | " <td>0.987747</td>\n", |
||
| 613 | " <td>0.943472</td>\n", |
||
| 614 | " <td>1</td>\n", |
||
| 615 | " </tr>\n", |
||
| 616 | " <tr>\n", |
||
| 617 | " <th>542757</th>\n", |
||
| 618 | " <td>22</td>\n", |
||
| 619 | " <td>rs142680588</td>\n", |
||
| 620 | " <td>51193629</td>\n", |
||
| 621 | " <td>G</td>\n", |
||
| 622 | " <td>A</td>\n", |
||
| 623 | " <td>9981</td>\n", |
||
| 624 | " <td>0.076595</td>\n", |
||
| 625 | " <td>-0.109532</td>\n", |
||
| 626 | " <td>0.312971</td>\n", |
||
| 627 | " <td>0.726358</td>\n", |
||
| 628 | " <td>52.471287</td>\n", |
||
| 629 | " <td>1.873861</td>\n", |
||
| 630 | " <td>0.122482</td>\n", |
||
| 631 | " <td>1.082649</td>\n", |
||
| 632 | " <td>0.26816</td>\n", |
||
| 633 | " <td>0.396718</td>\n", |
||
| 634 | " </tr>\n", |
||
| 635 | " </tbody>\n", |
||
| 636 | "</table>\n", |
||
| 637 | "<p>542758 rows × 16 columns</p>\n", |
||
| 638 | "</div>" |
||
| 639 | ], |
||
| 640 | "text/plain": [ |
||
| 641 | " #CHROM ID POS A1 A2 N AF1 BETA \\\n", |
||
| 642 | "0 1 rs3131962 756604 A G 9988 0.131007 -0.117134 \n", |
||
| 643 | "1 1 rs12562034 768448 A G 9978 0.104981 -0.064894 \n", |
||
| 644 | "2 1 rs4040617 779322 G A 9975 0.129123 -0.001462 \n", |
||
| 645 | "3 1 rs79373928 801536 G T 9994 0.014659 0.081544 \n", |
||
| 646 | "4 1 rs11240779 808631 G A 9919 0.226737 -0.184268 \n", |
||
| 647 | "... ... ... ... .. .. ... ... ... \n", |
||
| 648 | "542753 22 rs73174435 51174939 T C 9979 0.056118 -0.158762 \n", |
||
| 649 | "542754 22 rs3810648 51175626 G A 9931 0.058856 0.272493 \n", |
||
| 650 | "542755 22 rs5771002 51183255 A G 9840 0.333638 0.116325 \n", |
||
| 651 | "542756 22 rs3865764 51185848 G A 9974 0.051133 -0.026670 \n", |
||
| 652 | "542757 22 rs142680588 51193629 G A 9981 0.076595 -0.109532 \n", |
||
| 653 | "\n", |
||
| 654 | " SE P ld_score w_ld_score y pred \\\n", |
||
| 655 | "0 0.246231 0.634282 72.862240 4.474788 0.226298 1.082365 \n", |
||
| 656 | "1 0.273746 0.812611 34.749233 1.877341 0.056197 1.087724 \n", |
||
| 657 | "2 0.247254 0.995281 72.271390 4.208873 0.000035 1.058530 \n", |
||
| 658 | "3 0.688261 0.905688 16.740126 1.949177 0.014037 1.105125 \n", |
||
| 659 | "4 0.198982 0.354418 50.215000 2.825456 0.857575 1.081468 \n", |
||
| 660 | "... ... ... ... ... ... ... \n", |
||
| 661 | "542753 0.362390 0.661316 21.981667 1.363001 0.191929 1.008835 \n", |
||
| 662 | "542754 0.352508 0.439515 34.619377 1.804193 0.597548 1.034187 \n", |
||
| 663 | "542755 0.175675 0.507869 16.231083 1.273770 0.438456 1.093221 \n", |
||
| 664 | "542756 0.376132 0.943472 18.649513 1.010000 0.005028 0.987747 \n", |
||
| 665 | "542757 0.312971 0.726358 52.471287 1.873861 0.122482 1.082649 \n", |
||
| 666 | "\n", |
||
| 667 | " P_weighted KGWAS_P \n", |
||
| 668 | "0 0.234167 0.346428 \n", |
||
| 669 | "1 0.382894 0.566456 \n", |
||
| 670 | "2 0.995281 1 \n", |
||
| 671 | "3 0.225107 0.333025 \n", |
||
| 672 | "4 0.041646 0.061612 \n", |
||
| 673 | "... ... ... \n", |
||
| 674 | "542753 0.233609 0.345602 \n", |
||
| 675 | "542754 0.439515 0.650221 \n", |
||
| 676 | "542755 0.449038 0.66431 \n", |
||
| 677 | "542756 0.943472 1 \n", |
||
| 678 | "542757 0.26816 0.396718 \n", |
||
| 679 | "\n", |
||
| 680 | "[542758 rows x 16 columns]" |
||
| 681 | ] |
||
| 682 | }, |
||
| 683 | "execution_count": 5, |
||
| 684 | "metadata": {}, |
||
| 685 | "output_type": "execute_result" |
||
| 686 | } |
||
| 687 | ], |
||
| 688 | "source": [ |
||
| 689 | "run.kgwas_res" |
||
| 690 | ] |
||
| 691 | }, |
||
| 692 | { |
||
| 693 | "cell_type": "markdown", |
||
| 694 | "metadata": {}, |
||
| 695 | "source": [ |
||
| 696 | "If needed, you can load the pre-trained model via `run.load_pretrained()`." |
||
| 697 | ] |
||
| 698 | }, |
||
| 699 | { |
||
| 700 | "cell_type": "code", |
||
| 701 | "execution_count": null, |
||
| 702 | "metadata": {}, |
||
| 703 | "outputs": [], |
||
| 704 | "source": [ |
||
| 705 | "run.load_pretrained('./data/model/test')" |
||
| 706 | ] |
||
| 707 | }, |
||
| 708 | { |
||
| 709 | "cell_type": "markdown", |
||
| 710 | "metadata": {}, |
||
| 711 | "source": [ |
||
| 712 | "If you want to (1) use the full mode of KGWAS (i.e. larger node embeddings) or (2) access the null/causal simulations or (3) access the 21 subsampled GWAS sumstats across various sample sizes or (4) analyze the KGWAS sumstats for subsampled data or (5) analyze the KGWAS sumstats for all UKBB ICD10 diseases, please use [this link](https://drive.google.com/file/d/14UcHzPRIbdMmnLPZCHx_4G-gz2pipeg9/view?usp=sharing). Note that this file is large (around 45GB) and may take a while to download. After unzipping it, you can use that directory as the data directory for the KGWAS API." |
||
| 713 | ] |
||
| 714 | }, |
||
| 715 | { |
||
| 716 | "cell_type": "code", |
||
| 717 | "execution_count": 2, |
||
| 718 | "metadata": {}, |
||
| 719 | "outputs": [ |
||
| 720 | { |
||
| 721 | "name": "stdout", |
||
| 722 | "output_type": "stream", |
||
| 723 | "text": [ |
||
| 724 | "All required data files are present.\n" |
||
| 725 | ] |
||
| 726 | } |
||
| 727 | ], |
||
| 728 | "source": [ |
||
| 729 | "from kgwas import KGWAS, KGWAS_Data\n", |
||
| 730 | "data = KGWAS_Data(data_path = '/dfs/project/datasets/20220524-ukbiobank/data/kgwas_data/')" |
||
| 731 | ] |
||
| 732 | }, |
||
| 733 | { |
||
| 734 | "cell_type": "markdown", |
||
| 735 | "metadata": {}, |
||
| 736 | "source": [ |
||
| 737 | "Now that you can use various variant, gene, and program embeddings. For example, for the result in the paper, we use the baselineLD for variant and PoPS for gene." |
||
| 738 | ] |
||
| 739 | }, |
||
| 740 | { |
||
| 741 | "cell_type": "code", |
||
| 742 | "execution_count": 3, |
||
| 743 | "metadata": {}, |
||
| 744 | "outputs": [ |
||
| 745 | { |
||
| 746 | "name": "stdout", |
||
| 747 | "output_type": "stream", |
||
| 748 | "text": [ |
||
| 749 | "--loading KG---\n", |
||
| 750 | "--using baselineLD SNP embedding--\n", |
||
| 751 | "--using random go embedding--\n", |
||
| 752 | "--using PoPs expression+PPI+pathways gene embedding--\n" |
||
| 753 | ] |
||
| 754 | } |
||
| 755 | ], |
||
| 756 | "source": [ |
||
| 757 | "data.load_kg(snp_init_emb = 'baselineLD', \n", |
||
| 758 | " go_init_emb = 'random',\n", |
||
| 759 | " gene_init_emb = 'pops')" |
||
| 760 | ] |
||
| 761 | }, |
||
| 762 | { |
||
| 763 | "cell_type": "markdown", |
||
| 764 | "metadata": {}, |
||
| 765 | "source": [ |
||
| 766 | "There are many alternative embeddings as well. \n", |
||
| 767 | "- For variant: `enformer` (default), `baselineLD`, `SLDSC`, `cadd`, `kg`, `random`\n", |
||
| 768 | "- For gene: `esm` (default), `pops_expression`, `pops`, `kg`, `random`\n", |
||
| 769 | "- For program/go: `random` (default), `biogpt`, `kg`\n", |
||
| 770 | "\n", |
||
| 771 | "In additional to more embeddings, the full data folder contains summary statistics used in each analysis in the paper. For example, for the simulations, you can load it via:" |
||
| 772 | ] |
||
| 773 | }, |
||
| 774 | { |
||
| 775 | "cell_type": "code", |
||
| 776 | "execution_count": null, |
||
| 777 | "metadata": {}, |
||
| 778 | "outputs": [ |
||
| 779 | { |
||
| 780 | "name": "stdout", |
||
| 781 | "output_type": "stream", |
||
| 782 | "text": [ |
||
| 783 | "All required data files are present.\n", |
||
| 784 | "Using simulation data....\n" |
||
| 785 | ] |
||
| 786 | }, |
||
| 787 | { |
||
| 788 | "data": { |
||
| 789 | "text/html": [ |
||
| 790 | "<div>\n", |
||
| 791 | "<style scoped>\n", |
||
| 792 | " .dataframe tbody tr th:only-of-type {\n", |
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| 793 | " vertical-align: middle;\n", |
||
| 794 | " }\n", |
||
| 795 | "\n", |
||
| 796 | " .dataframe tbody tr th {\n", |
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| 797 | " vertical-align: top;\n", |
||
| 798 | " }\n", |
||
| 799 | "\n", |
||
| 800 | " .dataframe thead th {\n", |
||
| 801 | " text-align: right;\n", |
||
| 802 | " }\n", |
||
| 803 | "</style>\n", |
||
| 804 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 805 | " <thead>\n", |
||
| 806 | " <tr style=\"text-align: right;\">\n", |
||
| 807 | " <th></th>\n", |
||
| 808 | " <th>#CHROM</th>\n", |
||
| 809 | " <th>ID</th>\n", |
||
| 810 | " <th>POS</th>\n", |
||
| 811 | " <th>A1</th>\n", |
||
| 812 | " <th>A2</th>\n", |
||
| 813 | " <th>N</th>\n", |
||
| 814 | " <th>AF1</th>\n", |
||
| 815 | " <th>BETA</th>\n", |
||
| 816 | " <th>SE</th>\n", |
||
| 817 | " <th>P</th>\n", |
||
| 818 | " </tr>\n", |
||
| 819 | " </thead>\n", |
||
| 820 | " <tbody>\n", |
||
| 821 | " <tr>\n", |
||
| 822 | " <th>0</th>\n", |
||
| 823 | " <td>1</td>\n", |
||
| 824 | " <td>rs3131962</td>\n", |
||
| 825 | " <td>756604</td>\n", |
||
| 826 | " <td>A</td>\n", |
||
| 827 | " <td>G</td>\n", |
||
| 828 | " <td>4993</td>\n", |
||
| 829 | " <td>0.129882</td>\n", |
||
| 830 | " <td>14.559400</td>\n", |
||
| 831 | " <td>17.1871</td>\n", |
||
| 832 | " <td>0.396933</td>\n", |
||
| 833 | " </tr>\n", |
||
| 834 | " <tr>\n", |
||
| 835 | " <th>1</th>\n", |
||
| 836 | " <td>1</td>\n", |
||
| 837 | " <td>rs12562034</td>\n", |
||
| 838 | " <td>768448</td>\n", |
||
| 839 | " <td>A</td>\n", |
||
| 840 | " <td>G</td>\n", |
||
| 841 | " <td>4994</td>\n", |
||
| 842 | " <td>0.103124</td>\n", |
||
| 843 | " <td>-15.034400</td>\n", |
||
| 844 | " <td>19.0234</td>\n", |
||
| 845 | " <td>0.429345</td>\n", |
||
| 846 | " </tr>\n", |
||
| 847 | " <tr>\n", |
||
| 848 | " <th>2</th>\n", |
||
| 849 | " <td>1</td>\n", |
||
| 850 | " <td>rs4040617</td>\n", |
||
| 851 | " <td>779322</td>\n", |
||
| 852 | " <td>G</td>\n", |
||
| 853 | " <td>A</td>\n", |
||
| 854 | " <td>4979</td>\n", |
||
| 855 | " <td>0.127435</td>\n", |
||
| 856 | " <td>15.537200</td>\n", |
||
| 857 | " <td>17.3933</td>\n", |
||
| 858 | " <td>0.371704</td>\n", |
||
| 859 | " </tr>\n", |
||
| 860 | " <tr>\n", |
||
| 861 | " <th>3</th>\n", |
||
| 862 | " <td>1</td>\n", |
||
| 863 | " <td>rs79373928</td>\n", |
||
| 864 | " <td>801536</td>\n", |
||
| 865 | " <td>G</td>\n", |
||
| 866 | " <td>T</td>\n", |
||
| 867 | " <td>4996</td>\n", |
||
| 868 | " <td>0.015012</td>\n", |
||
| 869 | " <td>16.142600</td>\n", |
||
| 870 | " <td>47.7752</td>\n", |
||
| 871 | " <td>0.735448</td>\n", |
||
| 872 | " </tr>\n", |
||
| 873 | " <tr>\n", |
||
| 874 | " <th>4</th>\n", |
||
| 875 | " <td>1</td>\n", |
||
| 876 | " <td>rs11240779</td>\n", |
||
| 877 | " <td>808631</td>\n", |
||
| 878 | " <td>G</td>\n", |
||
| 879 | " <td>A</td>\n", |
||
| 880 | " <td>4961</td>\n", |
||
| 881 | " <td>0.222233</td>\n", |
||
| 882 | " <td>0.859838</td>\n", |
||
| 883 | " <td>13.9158</td>\n", |
||
| 884 | " <td>0.950731</td>\n", |
||
| 885 | " </tr>\n", |
||
| 886 | " <tr>\n", |
||
| 887 | " <th>...</th>\n", |
||
| 888 | " <td>...</td>\n", |
||
| 889 | " <td>...</td>\n", |
||
| 890 | " <td>...</td>\n", |
||
| 891 | " <td>...</td>\n", |
||
| 892 | " <td>...</td>\n", |
||
| 893 | " <td>...</td>\n", |
||
| 894 | " <td>...</td>\n", |
||
| 895 | " <td>...</td>\n", |
||
| 896 | " <td>...</td>\n", |
||
| 897 | " <td>...</td>\n", |
||
| 898 | " </tr>\n", |
||
| 899 | " <tr>\n", |
||
| 900 | " <th>542753</th>\n", |
||
| 901 | " <td>22</td>\n", |
||
| 902 | " <td>rs73174435</td>\n", |
||
| 903 | " <td>51174939</td>\n", |
||
| 904 | " <td>T</td>\n", |
||
| 905 | " <td>C</td>\n", |
||
| 906 | " <td>4991</td>\n", |
||
| 907 | " <td>0.057103</td>\n", |
||
| 908 | " <td>53.082400</td>\n", |
||
| 909 | " <td>24.8130</td>\n", |
||
| 910 | " <td>0.032412</td>\n", |
||
| 911 | " </tr>\n", |
||
| 912 | " <tr>\n", |
||
| 913 | " <th>542754</th>\n", |
||
| 914 | " <td>22</td>\n", |
||
| 915 | " <td>rs3810648</td>\n", |
||
| 916 | " <td>51175626</td>\n", |
||
| 917 | " <td>G</td>\n", |
||
| 918 | " <td>A</td>\n", |
||
| 919 | " <td>4959</td>\n", |
||
| 920 | " <td>0.066243</td>\n", |
||
| 921 | " <td>17.689800</td>\n", |
||
| 922 | " <td>23.2562</td>\n", |
||
| 923 | " <td>0.446867</td>\n", |
||
| 924 | " </tr>\n", |
||
| 925 | " <tr>\n", |
||
| 926 | " <th>542755</th>\n", |
||
| 927 | " <td>22</td>\n", |
||
| 928 | " <td>rs5771002</td>\n", |
||
| 929 | " <td>51183255</td>\n", |
||
| 930 | " <td>A</td>\n", |
||
| 931 | " <td>G</td>\n", |
||
| 932 | " <td>4937</td>\n", |
||
| 933 | " <td>0.334414</td>\n", |
||
| 934 | " <td>-12.170400</td>\n", |
||
| 935 | " <td>12.3314</td>\n", |
||
| 936 | " <td>0.323670</td>\n", |
||
| 937 | " </tr>\n", |
||
| 938 | " <tr>\n", |
||
| 939 | " <th>542756</th>\n", |
||
| 940 | " <td>22</td>\n", |
||
| 941 | " <td>rs3865764</td>\n", |
||
| 942 | " <td>51185848</td>\n", |
||
| 943 | " <td>G</td>\n", |
||
| 944 | " <td>A</td>\n", |
||
| 945 | " <td>4984</td>\n", |
||
| 946 | " <td>0.050662</td>\n", |
||
| 947 | " <td>-43.871900</td>\n", |
||
| 948 | " <td>26.3007</td>\n", |
||
| 949 | " <td>0.095299</td>\n", |
||
| 950 | " </tr>\n", |
||
| 951 | " <tr>\n", |
||
| 952 | " <th>542757</th>\n", |
||
| 953 | " <td>22</td>\n", |
||
| 954 | " <td>rs142680588</td>\n", |
||
| 955 | " <td>51193629</td>\n", |
||
| 956 | " <td>G</td>\n", |
||
| 957 | " <td>A</td>\n", |
||
| 958 | " <td>4994</td>\n", |
||
| 959 | " <td>0.073388</td>\n", |
||
| 960 | " <td>11.338700</td>\n", |
||
| 961 | " <td>22.2066</td>\n", |
||
| 962 | " <td>0.609630</td>\n", |
||
| 963 | " </tr>\n", |
||
| 964 | " </tbody>\n", |
||
| 965 | "</table>\n", |
||
| 966 | "<p>542758 rows × 10 columns</p>\n", |
||
| 967 | "</div>" |
||
| 968 | ], |
||
| 969 | "text/plain": [ |
||
| 970 | " #CHROM ID POS A1 A2 N AF1 BETA \\\n", |
||
| 971 | "0 1 rs3131962 756604 A G 4993 0.129882 14.559400 \n", |
||
| 972 | "1 1 rs12562034 768448 A G 4994 0.103124 -15.034400 \n", |
||
| 973 | "2 1 rs4040617 779322 G A 4979 0.127435 15.537200 \n", |
||
| 974 | "3 1 rs79373928 801536 G T 4996 0.015012 16.142600 \n", |
||
| 975 | "4 1 rs11240779 808631 G A 4961 0.222233 0.859838 \n", |
||
| 976 | "... ... ... ... .. .. ... ... ... \n", |
||
| 977 | "542753 22 rs73174435 51174939 T C 4991 0.057103 53.082400 \n", |
||
| 978 | "542754 22 rs3810648 51175626 G A 4959 0.066243 17.689800 \n", |
||
| 979 | "542755 22 rs5771002 51183255 A G 4937 0.334414 -12.170400 \n", |
||
| 980 | "542756 22 rs3865764 51185848 G A 4984 0.050662 -43.871900 \n", |
||
| 981 | "542757 22 rs142680588 51193629 G A 4994 0.073388 11.338700 \n", |
||
| 982 | "\n", |
||
| 983 | " SE P \n", |
||
| 984 | "0 17.1871 0.396933 \n", |
||
| 985 | "1 19.0234 0.429345 \n", |
||
| 986 | "2 17.3933 0.371704 \n", |
||
| 987 | "3 47.7752 0.735448 \n", |
||
| 988 | "4 13.9158 0.950731 \n", |
||
| 989 | "... ... ... \n", |
||
| 990 | "542753 24.8130 0.032412 \n", |
||
| 991 | "542754 23.2562 0.446867 \n", |
||
| 992 | "542755 12.3314 0.323670 \n", |
||
| 993 | "542756 26.3007 0.095299 \n", |
||
| 994 | "542757 22.2066 0.609630 \n", |
||
| 995 | "\n", |
||
| 996 | "[542758 rows x 10 columns]" |
||
| 997 | ] |
||
| 998 | }, |
||
| 999 | "execution_count": 1, |
||
| 1000 | "metadata": {}, |
||
| 1001 | "output_type": "execute_result" |
||
| 1002 | } |
||
| 1003 | ], |
||
| 1004 | "source": [ |
||
| 1005 | "data.load_simulation_gwas('causal', seed = 1) # seed can range from 1-500\n", |
||
| 1006 | "data.lr_uni" |
||
| 1007 | ] |
||
| 1008 | }, |
||
| 1009 | { |
||
| 1010 | "cell_type": "markdown", |
||
| 1011 | "metadata": {}, |
||
| 1012 | "source": [ |
||
| 1013 | "Similarly for null simulations, you can load it via:" |
||
| 1014 | ] |
||
| 1015 | }, |
||
| 1016 | { |
||
| 1017 | "cell_type": "code", |
||
| 1018 | "execution_count": 2, |
||
| 1019 | "metadata": {}, |
||
| 1020 | "outputs": [ |
||
| 1021 | { |
||
| 1022 | "name": "stdout", |
||
| 1023 | "output_type": "stream", |
||
| 1024 | "text": [ |
||
| 1025 | "Using simulation data....\n" |
||
| 1026 | ] |
||
| 1027 | }, |
||
| 1028 | { |
||
| 1029 | "data": { |
||
| 1030 | "text/html": [ |
||
| 1031 | "<div>\n", |
||
| 1032 | "<style scoped>\n", |
||
| 1033 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1034 | " vertical-align: middle;\n", |
||
| 1035 | " }\n", |
||
| 1036 | "\n", |
||
| 1037 | " .dataframe tbody tr th {\n", |
||
| 1038 | " vertical-align: top;\n", |
||
| 1039 | " }\n", |
||
| 1040 | "\n", |
||
| 1041 | " .dataframe thead th {\n", |
||
| 1042 | " text-align: right;\n", |
||
| 1043 | " }\n", |
||
| 1044 | "</style>\n", |
||
| 1045 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1046 | " <thead>\n", |
||
| 1047 | " <tr style=\"text-align: right;\">\n", |
||
| 1048 | " <th></th>\n", |
||
| 1049 | " <th>#CHROM</th>\n", |
||
| 1050 | " <th>ID</th>\n", |
||
| 1051 | " <th>POS</th>\n", |
||
| 1052 | " <th>A1</th>\n", |
||
| 1053 | " <th>A2</th>\n", |
||
| 1054 | " <th>N</th>\n", |
||
| 1055 | " <th>AF1</th>\n", |
||
| 1056 | " <th>BETA</th>\n", |
||
| 1057 | " <th>SE</th>\n", |
||
| 1058 | " <th>P</th>\n", |
||
| 1059 | " </tr>\n", |
||
| 1060 | " </thead>\n", |
||
| 1061 | " <tbody>\n", |
||
| 1062 | " <tr>\n", |
||
| 1063 | " <th>0</th>\n", |
||
| 1064 | " <td>1</td>\n", |
||
| 1065 | " <td>rs3131962</td>\n", |
||
| 1066 | " <td>756604</td>\n", |
||
| 1067 | " <td>A</td>\n", |
||
| 1068 | " <td>G</td>\n", |
||
| 1069 | " <td>4993</td>\n", |
||
| 1070 | " <td>0.129882</td>\n", |
||
| 1071 | " <td>-2.960260</td>\n", |
||
| 1072 | " <td>7.66276</td>\n", |
||
| 1073 | " <td>0.699261</td>\n", |
||
| 1074 | " </tr>\n", |
||
| 1075 | " <tr>\n", |
||
| 1076 | " <th>1</th>\n", |
||
| 1077 | " <td>1</td>\n", |
||
| 1078 | " <td>rs12562034</td>\n", |
||
| 1079 | " <td>768448</td>\n", |
||
| 1080 | " <td>A</td>\n", |
||
| 1081 | " <td>G</td>\n", |
||
| 1082 | " <td>4994</td>\n", |
||
| 1083 | " <td>0.103124</td>\n", |
||
| 1084 | " <td>-19.335700</td>\n", |
||
| 1085 | " <td>8.47710</td>\n", |
||
| 1086 | " <td>0.022552</td>\n", |
||
| 1087 | " </tr>\n", |
||
| 1088 | " <tr>\n", |
||
| 1089 | " <th>2</th>\n", |
||
| 1090 | " <td>1</td>\n", |
||
| 1091 | " <td>rs4040617</td>\n", |
||
| 1092 | " <td>779322</td>\n", |
||
| 1093 | " <td>G</td>\n", |
||
| 1094 | " <td>A</td>\n", |
||
| 1095 | " <td>4979</td>\n", |
||
| 1096 | " <td>0.127435</td>\n", |
||
| 1097 | " <td>-3.287600</td>\n", |
||
| 1098 | " <td>7.75475</td>\n", |
||
| 1099 | " <td>0.671605</td>\n", |
||
| 1100 | " </tr>\n", |
||
| 1101 | " <tr>\n", |
||
| 1102 | " <th>3</th>\n", |
||
| 1103 | " <td>1</td>\n", |
||
| 1104 | " <td>rs79373928</td>\n", |
||
| 1105 | " <td>801536</td>\n", |
||
| 1106 | " <td>G</td>\n", |
||
| 1107 | " <td>T</td>\n", |
||
| 1108 | " <td>4996</td>\n", |
||
| 1109 | " <td>0.015012</td>\n", |
||
| 1110 | " <td>-12.530000</td>\n", |
||
| 1111 | " <td>21.29860</td>\n", |
||
| 1112 | " <td>0.556329</td>\n", |
||
| 1113 | " </tr>\n", |
||
| 1114 | " <tr>\n", |
||
| 1115 | " <th>4</th>\n", |
||
| 1116 | " <td>1</td>\n", |
||
| 1117 | " <td>rs11240779</td>\n", |
||
| 1118 | " <td>808631</td>\n", |
||
| 1119 | " <td>G</td>\n", |
||
| 1120 | " <td>A</td>\n", |
||
| 1121 | " <td>4961</td>\n", |
||
| 1122 | " <td>0.222233</td>\n", |
||
| 1123 | " <td>-8.564830</td>\n", |
||
| 1124 | " <td>6.20273</td>\n", |
||
| 1125 | " <td>0.167335</td>\n", |
||
| 1126 | " </tr>\n", |
||
| 1127 | " <tr>\n", |
||
| 1128 | " <th>...</th>\n", |
||
| 1129 | " <td>...</td>\n", |
||
| 1130 | " <td>...</td>\n", |
||
| 1131 | " <td>...</td>\n", |
||
| 1132 | " <td>...</td>\n", |
||
| 1133 | " <td>...</td>\n", |
||
| 1134 | " <td>...</td>\n", |
||
| 1135 | " <td>...</td>\n", |
||
| 1136 | " <td>...</td>\n", |
||
| 1137 | " <td>...</td>\n", |
||
| 1138 | " <td>...</td>\n", |
||
| 1139 | " </tr>\n", |
||
| 1140 | " <tr>\n", |
||
| 1141 | " <th>542753</th>\n", |
||
| 1142 | " <td>22</td>\n", |
||
| 1143 | " <td>rs73174435</td>\n", |
||
| 1144 | " <td>51174939</td>\n", |
||
| 1145 | " <td>T</td>\n", |
||
| 1146 | " <td>C</td>\n", |
||
| 1147 | " <td>4991</td>\n", |
||
| 1148 | " <td>0.057103</td>\n", |
||
| 1149 | " <td>-24.859400</td>\n", |
||
| 1150 | " <td>11.06160</td>\n", |
||
| 1151 | " <td>0.024617</td>\n", |
||
| 1152 | " </tr>\n", |
||
| 1153 | " <tr>\n", |
||
| 1154 | " <th>542754</th>\n", |
||
| 1155 | " <td>22</td>\n", |
||
| 1156 | " <td>rs3810648</td>\n", |
||
| 1157 | " <td>51175626</td>\n", |
||
| 1158 | " <td>G</td>\n", |
||
| 1159 | " <td>A</td>\n", |
||
| 1160 | " <td>4959</td>\n", |
||
| 1161 | " <td>0.066243</td>\n", |
||
| 1162 | " <td>-0.725793</td>\n", |
||
| 1163 | " <td>10.36870</td>\n", |
||
| 1164 | " <td>0.944195</td>\n", |
||
| 1165 | " </tr>\n", |
||
| 1166 | " <tr>\n", |
||
| 1167 | " <th>542755</th>\n", |
||
| 1168 | " <td>22</td>\n", |
||
| 1169 | " <td>rs5771002</td>\n", |
||
| 1170 | " <td>51183255</td>\n", |
||
| 1171 | " <td>A</td>\n", |
||
| 1172 | " <td>G</td>\n", |
||
| 1173 | " <td>4937</td>\n", |
||
| 1174 | " <td>0.334414</td>\n", |
||
| 1175 | " <td>-5.555300</td>\n", |
||
| 1176 | " <td>5.49753</td>\n", |
||
| 1177 | " <td>0.312251</td>\n", |
||
| 1178 | " </tr>\n", |
||
| 1179 | " <tr>\n", |
||
| 1180 | " <th>542756</th>\n", |
||
| 1181 | " <td>22</td>\n", |
||
| 1182 | " <td>rs3865764</td>\n", |
||
| 1183 | " <td>51185848</td>\n", |
||
| 1184 | " <td>G</td>\n", |
||
| 1185 | " <td>A</td>\n", |
||
| 1186 | " <td>4984</td>\n", |
||
| 1187 | " <td>0.050662</td>\n", |
||
| 1188 | " <td>12.588200</td>\n", |
||
| 1189 | " <td>11.72730</td>\n", |
||
| 1190 | " <td>0.283085</td>\n", |
||
| 1191 | " </tr>\n", |
||
| 1192 | " <tr>\n", |
||
| 1193 | " <th>542757</th>\n", |
||
| 1194 | " <td>22</td>\n", |
||
| 1195 | " <td>rs142680588</td>\n", |
||
| 1196 | " <td>51193629</td>\n", |
||
| 1197 | " <td>G</td>\n", |
||
| 1198 | " <td>A</td>\n", |
||
| 1199 | " <td>4994</td>\n", |
||
| 1200 | " <td>0.073388</td>\n", |
||
| 1201 | " <td>-13.533700</td>\n", |
||
| 1202 | " <td>9.89851</td>\n", |
||
| 1203 | " <td>0.171548</td>\n", |
||
| 1204 | " </tr>\n", |
||
| 1205 | " </tbody>\n", |
||
| 1206 | "</table>\n", |
||
| 1207 | "<p>542758 rows × 10 columns</p>\n", |
||
| 1208 | "</div>" |
||
| 1209 | ], |
||
| 1210 | "text/plain": [ |
||
| 1211 | " #CHROM ID POS A1 A2 N AF1 BETA \\\n", |
||
| 1212 | "0 1 rs3131962 756604 A G 4993 0.129882 -2.960260 \n", |
||
| 1213 | "1 1 rs12562034 768448 A G 4994 0.103124 -19.335700 \n", |
||
| 1214 | "2 1 rs4040617 779322 G A 4979 0.127435 -3.287600 \n", |
||
| 1215 | "3 1 rs79373928 801536 G T 4996 0.015012 -12.530000 \n", |
||
| 1216 | "4 1 rs11240779 808631 G A 4961 0.222233 -8.564830 \n", |
||
| 1217 | "... ... ... ... .. .. ... ... ... \n", |
||
| 1218 | "542753 22 rs73174435 51174939 T C 4991 0.057103 -24.859400 \n", |
||
| 1219 | "542754 22 rs3810648 51175626 G A 4959 0.066243 -0.725793 \n", |
||
| 1220 | "542755 22 rs5771002 51183255 A G 4937 0.334414 -5.555300 \n", |
||
| 1221 | "542756 22 rs3865764 51185848 G A 4984 0.050662 12.588200 \n", |
||
| 1222 | "542757 22 rs142680588 51193629 G A 4994 0.073388 -13.533700 \n", |
||
| 1223 | "\n", |
||
| 1224 | " SE P \n", |
||
| 1225 | "0 7.66276 0.699261 \n", |
||
| 1226 | "1 8.47710 0.022552 \n", |
||
| 1227 | "2 7.75475 0.671605 \n", |
||
| 1228 | "3 21.29860 0.556329 \n", |
||
| 1229 | "4 6.20273 0.167335 \n", |
||
| 1230 | "... ... ... \n", |
||
| 1231 | "542753 11.06160 0.024617 \n", |
||
| 1232 | "542754 10.36870 0.944195 \n", |
||
| 1233 | "542755 5.49753 0.312251 \n", |
||
| 1234 | "542756 11.72730 0.283085 \n", |
||
| 1235 | "542757 9.89851 0.171548 \n", |
||
| 1236 | "\n", |
||
| 1237 | "[542758 rows x 10 columns]" |
||
| 1238 | ] |
||
| 1239 | }, |
||
| 1240 | "execution_count": 2, |
||
| 1241 | "metadata": {}, |
||
| 1242 | "output_type": "execute_result" |
||
| 1243 | } |
||
| 1244 | ], |
||
| 1245 | "source": [ |
||
| 1246 | "data.load_simulation_gwas('null', seed = 1)# seed can range from 1-500\n", |
||
| 1247 | "data.lr_uni" |
||
| 1248 | ] |
||
| 1249 | }, |
||
| 1250 | { |
||
| 1251 | "cell_type": "markdown", |
||
| 1252 | "metadata": {}, |
||
| 1253 | "source": [ |
||
| 1254 | "Now, for the subsampling analysis, you can load any trait out of the 21 subsampled traits in various sample sizes across 5 replicates. The phenotype list can be accessed via:" |
||
| 1255 | ] |
||
| 1256 | }, |
||
| 1257 | { |
||
| 1258 | "cell_type": "code", |
||
| 1259 | "execution_count": 3, |
||
| 1260 | "metadata": {}, |
||
| 1261 | "outputs": [ |
||
| 1262 | { |
||
| 1263 | "data": { |
||
| 1264 | "text/plain": [ |
||
| 1265 | "['body_BALDING1',\n", |
||
| 1266 | " 'disease_ALLERGY_ECZEMA_DIAGNOSED',\n", |
||
| 1267 | " 'disease_HYPOTHYROIDISM_SELF_REP',\n", |
||
| 1268 | " 'pigment_SUNBURN',\n", |
||
| 1269 | " '21001',\n", |
||
| 1270 | " '50',\n", |
||
| 1271 | " '30080',\n", |
||
| 1272 | " '30070',\n", |
||
| 1273 | " '30010',\n", |
||
| 1274 | " '30000',\n", |
||
| 1275 | " 'biochemistry_AlkalinePhosphatase',\n", |
||
| 1276 | " 'biochemistry_AspartateAminotransferase',\n", |
||
| 1277 | " 'biochemistry_Cholesterol',\n", |
||
| 1278 | " 'biochemistry_Creatinine',\n", |
||
| 1279 | " 'biochemistry_IGF1',\n", |
||
| 1280 | " 'biochemistry_Phosphate',\n", |
||
| 1281 | " 'biochemistry_Testosterone_Male',\n", |
||
| 1282 | " 'biochemistry_TotalBilirubin',\n", |
||
| 1283 | " 'biochemistry_TotalProtein',\n", |
||
| 1284 | " 'biochemistry_VitaminD',\n", |
||
| 1285 | " 'bmd_HEEL_TSCOREz']" |
||
| 1286 | ] |
||
| 1287 | }, |
||
| 1288 | "execution_count": 3, |
||
| 1289 | "metadata": {}, |
||
| 1290 | "output_type": "execute_result" |
||
| 1291 | } |
||
| 1292 | ], |
||
| 1293 | "source": [ |
||
| 1294 | "data.get_pheno_list()['21_indep_traits']" |
||
| 1295 | ] |
||
| 1296 | }, |
||
| 1297 | { |
||
| 1298 | "cell_type": "markdown", |
||
| 1299 | "metadata": {}, |
||
| 1300 | "source": [ |
||
| 1301 | "Usually each trait has the following sample sizes available: 1000, 2500, 5000, 7500, 10000, 50000, 100000, 200000. For example, to load body_BALDING1 at sample size 1000 at replicate 1, you can use:" |
||
| 1302 | ] |
||
| 1303 | }, |
||
| 1304 | { |
||
| 1305 | "cell_type": "code", |
||
| 1306 | "execution_count": 4, |
||
| 1307 | "metadata": {}, |
||
| 1308 | "outputs": [ |
||
| 1309 | { |
||
| 1310 | "data": { |
||
| 1311 | "text/html": [ |
||
| 1312 | "<div>\n", |
||
| 1313 | "<style scoped>\n", |
||
| 1314 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1315 | " vertical-align: middle;\n", |
||
| 1316 | " }\n", |
||
| 1317 | "\n", |
||
| 1318 | " .dataframe tbody tr th {\n", |
||
| 1319 | " vertical-align: top;\n", |
||
| 1320 | " }\n", |
||
| 1321 | "\n", |
||
| 1322 | " .dataframe thead th {\n", |
||
| 1323 | " text-align: right;\n", |
||
| 1324 | " }\n", |
||
| 1325 | "</style>\n", |
||
| 1326 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1327 | " <thead>\n", |
||
| 1328 | " <tr style=\"text-align: right;\">\n", |
||
| 1329 | " <th></th>\n", |
||
| 1330 | " <th>#CHROM</th>\n", |
||
| 1331 | " <th>POS</th>\n", |
||
| 1332 | " <th>ID</th>\n", |
||
| 1333 | " <th>REF</th>\n", |
||
| 1334 | " <th>ALT</th>\n", |
||
| 1335 | " <th>A1</th>\n", |
||
| 1336 | " <th>FIRTH?</th>\n", |
||
| 1337 | " <th>TEST</th>\n", |
||
| 1338 | " <th>OBS_CT</th>\n", |
||
| 1339 | " <th>OR</th>\n", |
||
| 1340 | " <th>LOG(OR)_SE</th>\n", |
||
| 1341 | " <th>Z_STAT</th>\n", |
||
| 1342 | " <th>P</th>\n", |
||
| 1343 | " <th>ERRCODE</th>\n", |
||
| 1344 | " <th>SNP</th>\n", |
||
| 1345 | " <th>A2</th>\n", |
||
| 1346 | " <th>N</th>\n", |
||
| 1347 | " </tr>\n", |
||
| 1348 | " </thead>\n", |
||
| 1349 | " <tbody>\n", |
||
| 1350 | " <tr>\n", |
||
| 1351 | " <th>0</th>\n", |
||
| 1352 | " <td>1</td>\n", |
||
| 1353 | " <td>756604</td>\n", |
||
| 1354 | " <td>rs3131962</td>\n", |
||
| 1355 | " <td>G</td>\n", |
||
| 1356 | " <td>A</td>\n", |
||
| 1357 | " <td>A</td>\n", |
||
| 1358 | " <td>Y</td>\n", |
||
| 1359 | " <td>ADD</td>\n", |
||
| 1360 | " <td>999</td>\n", |
||
| 1361 | " <td>1.241130</td>\n", |
||
| 1362 | " <td>0.209870</td>\n", |
||
| 1363 | " <td>1.029320</td>\n", |
||
| 1364 | " <td>0.303330</td>\n", |
||
| 1365 | " <td>.</td>\n", |
||
| 1366 | " <td>rs3131962</td>\n", |
||
| 1367 | " <td>G</td>\n", |
||
| 1368 | " <td>999</td>\n", |
||
| 1369 | " </tr>\n", |
||
| 1370 | " <tr>\n", |
||
| 1371 | " <th>1</th>\n", |
||
| 1372 | " <td>1</td>\n", |
||
| 1373 | " <td>768448</td>\n", |
||
| 1374 | " <td>rs12562034</td>\n", |
||
| 1375 | " <td>G</td>\n", |
||
| 1376 | " <td>A</td>\n", |
||
| 1377 | " <td>A</td>\n", |
||
| 1378 | " <td>Y</td>\n", |
||
| 1379 | " <td>ADD</td>\n", |
||
| 1380 | " <td>996</td>\n", |
||
| 1381 | " <td>0.433894</td>\n", |
||
| 1382 | " <td>0.285912</td>\n", |
||
| 1383 | " <td>-2.920330</td>\n", |
||
| 1384 | " <td>0.003497</td>\n", |
||
| 1385 | " <td>.</td>\n", |
||
| 1386 | " <td>rs12562034</td>\n", |
||
| 1387 | " <td>G</td>\n", |
||
| 1388 | " <td>996</td>\n", |
||
| 1389 | " </tr>\n", |
||
| 1390 | " <tr>\n", |
||
| 1391 | " <th>2</th>\n", |
||
| 1392 | " <td>1</td>\n", |
||
| 1393 | " <td>779322</td>\n", |
||
| 1394 | " <td>rs4040617</td>\n", |
||
| 1395 | " <td>A</td>\n", |
||
| 1396 | " <td>G</td>\n", |
||
| 1397 | " <td>G</td>\n", |
||
| 1398 | " <td>Y</td>\n", |
||
| 1399 | " <td>ADD</td>\n", |
||
| 1400 | " <td>996</td>\n", |
||
| 1401 | " <td>1.178310</td>\n", |
||
| 1402 | " <td>0.211892</td>\n", |
||
| 1403 | " <td>0.774379</td>\n", |
||
| 1404 | " <td>0.438707</td>\n", |
||
| 1405 | " <td>.</td>\n", |
||
| 1406 | " <td>rs4040617</td>\n", |
||
| 1407 | " <td>A</td>\n", |
||
| 1408 | " <td>996</td>\n", |
||
| 1409 | " </tr>\n", |
||
| 1410 | " <tr>\n", |
||
| 1411 | " <th>3</th>\n", |
||
| 1412 | " <td>1</td>\n", |
||
| 1413 | " <td>801536</td>\n", |
||
| 1414 | " <td>rs79373928</td>\n", |
||
| 1415 | " <td>T</td>\n", |
||
| 1416 | " <td>G</td>\n", |
||
| 1417 | " <td>G</td>\n", |
||
| 1418 | " <td>Y</td>\n", |
||
| 1419 | " <td>ADD</td>\n", |
||
| 1420 | " <td>998</td>\n", |
||
| 1421 | " <td>0.989852</td>\n", |
||
| 1422 | " <td>0.479159</td>\n", |
||
| 1423 | " <td>-0.021286</td>\n", |
||
| 1424 | " <td>0.983018</td>\n", |
||
| 1425 | " <td>.</td>\n", |
||
| 1426 | " <td>rs79373928</td>\n", |
||
| 1427 | " <td>T</td>\n", |
||
| 1428 | " <td>998</td>\n", |
||
| 1429 | " </tr>\n", |
||
| 1430 | " <tr>\n", |
||
| 1431 | " <th>4</th>\n", |
||
| 1432 | " <td>1</td>\n", |
||
| 1433 | " <td>808631</td>\n", |
||
| 1434 | " <td>rs11240779</td>\n", |
||
| 1435 | " <td>A</td>\n", |
||
| 1436 | " <td>G</td>\n", |
||
| 1437 | " <td>G</td>\n", |
||
| 1438 | " <td>Y</td>\n", |
||
| 1439 | " <td>ADD</td>\n", |
||
| 1440 | " <td>994</td>\n", |
||
| 1441 | " <td>0.880382</td>\n", |
||
| 1442 | " <td>0.173114</td>\n", |
||
| 1443 | " <td>-0.735930</td>\n", |
||
| 1444 | " <td>0.461773</td>\n", |
||
| 1445 | " <td>.</td>\n", |
||
| 1446 | " <td>rs11240779</td>\n", |
||
| 1447 | " <td>A</td>\n", |
||
| 1448 | " <td>994</td>\n", |
||
| 1449 | " </tr>\n", |
||
| 1450 | " <tr>\n", |
||
| 1451 | " <th>...</th>\n", |
||
| 1452 | " <td>...</td>\n", |
||
| 1453 | " <td>...</td>\n", |
||
| 1454 | " <td>...</td>\n", |
||
| 1455 | " <td>...</td>\n", |
||
| 1456 | " <td>...</td>\n", |
||
| 1457 | " <td>...</td>\n", |
||
| 1458 | " <td>...</td>\n", |
||
| 1459 | " <td>...</td>\n", |
||
| 1460 | " <td>...</td>\n", |
||
| 1461 | " <td>...</td>\n", |
||
| 1462 | " <td>...</td>\n", |
||
| 1463 | " <td>...</td>\n", |
||
| 1464 | " <td>...</td>\n", |
||
| 1465 | " <td>...</td>\n", |
||
| 1466 | " <td>...</td>\n", |
||
| 1467 | " <td>...</td>\n", |
||
| 1468 | " <td>...</td>\n", |
||
| 1469 | " </tr>\n", |
||
| 1470 | " <tr>\n", |
||
| 1471 | " <th>542753</th>\n", |
||
| 1472 | " <td>22</td>\n", |
||
| 1473 | " <td>51174939</td>\n", |
||
| 1474 | " <td>rs73174435</td>\n", |
||
| 1475 | " <td>C</td>\n", |
||
| 1476 | " <td>T</td>\n", |
||
| 1477 | " <td>T</td>\n", |
||
| 1478 | " <td>Y</td>\n", |
||
| 1479 | " <td>ADD</td>\n", |
||
| 1480 | " <td>999</td>\n", |
||
| 1481 | " <td>0.642727</td>\n", |
||
| 1482 | " <td>0.362564</td>\n", |
||
| 1483 | " <td>-1.219190</td>\n", |
||
| 1484 | " <td>0.222772</td>\n", |
||
| 1485 | " <td>.</td>\n", |
||
| 1486 | " <td>rs73174435</td>\n", |
||
| 1487 | " <td>C</td>\n", |
||
| 1488 | " <td>999</td>\n", |
||
| 1489 | " </tr>\n", |
||
| 1490 | " <tr>\n", |
||
| 1491 | " <th>542754</th>\n", |
||
| 1492 | " <td>22</td>\n", |
||
| 1493 | " <td>51175626</td>\n", |
||
| 1494 | " <td>rs3810648</td>\n", |
||
| 1495 | " <td>A</td>\n", |
||
| 1496 | " <td>G</td>\n", |
||
| 1497 | " <td>G</td>\n", |
||
| 1498 | " <td>Y</td>\n", |
||
| 1499 | " <td>ADD</td>\n", |
||
| 1500 | " <td>996</td>\n", |
||
| 1501 | " <td>0.752885</td>\n", |
||
| 1502 | " <td>0.286799</td>\n", |
||
| 1503 | " <td>-0.989690</td>\n", |
||
| 1504 | " <td>0.322326</td>\n", |
||
| 1505 | " <td>.</td>\n", |
||
| 1506 | " <td>rs3810648</td>\n", |
||
| 1507 | " <td>A</td>\n", |
||
| 1508 | " <td>996</td>\n", |
||
| 1509 | " </tr>\n", |
||
| 1510 | " <tr>\n", |
||
| 1511 | " <th>542755</th>\n", |
||
| 1512 | " <td>22</td>\n", |
||
| 1513 | " <td>51183255</td>\n", |
||
| 1514 | " <td>rs5771002</td>\n", |
||
| 1515 | " <td>G</td>\n", |
||
| 1516 | " <td>A</td>\n", |
||
| 1517 | " <td>A</td>\n", |
||
| 1518 | " <td>Y</td>\n", |
||
| 1519 | " <td>ADD</td>\n", |
||
| 1520 | " <td>981</td>\n", |
||
| 1521 | " <td>0.792577</td>\n", |
||
| 1522 | " <td>0.150356</td>\n", |
||
| 1523 | " <td>-1.546100</td>\n", |
||
| 1524 | " <td>0.122080</td>\n", |
||
| 1525 | " <td>.</td>\n", |
||
| 1526 | " <td>rs5771002</td>\n", |
||
| 1527 | " <td>G</td>\n", |
||
| 1528 | " <td>981</td>\n", |
||
| 1529 | " </tr>\n", |
||
| 1530 | " <tr>\n", |
||
| 1531 | " <th>542756</th>\n", |
||
| 1532 | " <td>22</td>\n", |
||
| 1533 | " <td>51185848</td>\n", |
||
| 1534 | " <td>rs3865764</td>\n", |
||
| 1535 | " <td>A</td>\n", |
||
| 1536 | " <td>G</td>\n", |
||
| 1537 | " <td>G</td>\n", |
||
| 1538 | " <td>Y</td>\n", |
||
| 1539 | " <td>ADD</td>\n", |
||
| 1540 | " <td>996</td>\n", |
||
| 1541 | " <td>1.004930</td>\n", |
||
| 1542 | " <td>0.386700</td>\n", |
||
| 1543 | " <td>0.012715</td>\n", |
||
| 1544 | " <td>0.989855</td>\n", |
||
| 1545 | " <td>.</td>\n", |
||
| 1546 | " <td>rs3865764</td>\n", |
||
| 1547 | " <td>A</td>\n", |
||
| 1548 | " <td>996</td>\n", |
||
| 1549 | " </tr>\n", |
||
| 1550 | " <tr>\n", |
||
| 1551 | " <th>542757</th>\n", |
||
| 1552 | " <td>22</td>\n", |
||
| 1553 | " <td>51193629</td>\n", |
||
| 1554 | " <td>rs142680588</td>\n", |
||
| 1555 | " <td>A</td>\n", |
||
| 1556 | " <td>G</td>\n", |
||
| 1557 | " <td>G</td>\n", |
||
| 1558 | " <td>Y</td>\n", |
||
| 1559 | " <td>ADD</td>\n", |
||
| 1560 | " <td>1000</td>\n", |
||
| 1561 | " <td>1.497360</td>\n", |
||
| 1562 | " <td>0.267489</td>\n", |
||
| 1563 | " <td>1.509230</td>\n", |
||
| 1564 | " <td>0.131240</td>\n", |
||
| 1565 | " <td>.</td>\n", |
||
| 1566 | " <td>rs142680588</td>\n", |
||
| 1567 | " <td>A</td>\n", |
||
| 1568 | " <td>1000</td>\n", |
||
| 1569 | " </tr>\n", |
||
| 1570 | " </tbody>\n", |
||
| 1571 | "</table>\n", |
||
| 1572 | "<p>542758 rows × 17 columns</p>\n", |
||
| 1573 | "</div>" |
||
| 1574 | ], |
||
| 1575 | "text/plain": [ |
||
| 1576 | " #CHROM POS ID REF ALT A1 FIRTH? TEST OBS_CT \\\n", |
||
| 1577 | "0 1 756604 rs3131962 G A A Y ADD 999 \n", |
||
| 1578 | "1 1 768448 rs12562034 G A A Y ADD 996 \n", |
||
| 1579 | "2 1 779322 rs4040617 A G G Y ADD 996 \n", |
||
| 1580 | "3 1 801536 rs79373928 T G G Y ADD 998 \n", |
||
| 1581 | "4 1 808631 rs11240779 A G G Y ADD 994 \n", |
||
| 1582 | "... ... ... ... .. .. .. ... ... ... \n", |
||
| 1583 | "542753 22 51174939 rs73174435 C T T Y ADD 999 \n", |
||
| 1584 | "542754 22 51175626 rs3810648 A G G Y ADD 996 \n", |
||
| 1585 | "542755 22 51183255 rs5771002 G A A Y ADD 981 \n", |
||
| 1586 | "542756 22 51185848 rs3865764 A G G Y ADD 996 \n", |
||
| 1587 | "542757 22 51193629 rs142680588 A G G Y ADD 1000 \n", |
||
| 1588 | "\n", |
||
| 1589 | " OR LOG(OR)_SE Z_STAT P ERRCODE SNP A2 N \n", |
||
| 1590 | "0 1.241130 0.209870 1.029320 0.303330 . rs3131962 G 999 \n", |
||
| 1591 | "1 0.433894 0.285912 -2.920330 0.003497 . rs12562034 G 996 \n", |
||
| 1592 | "2 1.178310 0.211892 0.774379 0.438707 . rs4040617 A 996 \n", |
||
| 1593 | "3 0.989852 0.479159 -0.021286 0.983018 . rs79373928 T 998 \n", |
||
| 1594 | "4 0.880382 0.173114 -0.735930 0.461773 . rs11240779 A 994 \n", |
||
| 1595 | "... ... ... ... ... ... ... .. ... \n", |
||
| 1596 | "542753 0.642727 0.362564 -1.219190 0.222772 . rs73174435 C 999 \n", |
||
| 1597 | "542754 0.752885 0.286799 -0.989690 0.322326 . rs3810648 A 996 \n", |
||
| 1598 | "542755 0.792577 0.150356 -1.546100 0.122080 . rs5771002 G 981 \n", |
||
| 1599 | "542756 1.004930 0.386700 0.012715 0.989855 . rs3865764 A 996 \n", |
||
| 1600 | "542757 1.497360 0.267489 1.509230 0.131240 . rs142680588 A 1000 \n", |
||
| 1601 | "\n", |
||
| 1602 | "[542758 rows x 17 columns]" |
||
| 1603 | ] |
||
| 1604 | }, |
||
| 1605 | "execution_count": 4, |
||
| 1606 | "metadata": {}, |
||
| 1607 | "output_type": "execute_result" |
||
| 1608 | } |
||
| 1609 | ], |
||
| 1610 | "source": [ |
||
| 1611 | "data.load_gwas_subsample(pheno = 'body_BALDING1', sample_size = 1000, seed = 1)\n", |
||
| 1612 | "data.lr_uni" |
||
| 1613 | ] |
||
| 1614 | }, |
||
| 1615 | { |
||
| 1616 | "cell_type": "markdown", |
||
| 1617 | "metadata": {}, |
||
| 1618 | "source": [ |
||
| 1619 | "You can also load the full cohort GWAS for these 21 traits via:" |
||
| 1620 | ] |
||
| 1621 | }, |
||
| 1622 | { |
||
| 1623 | "cell_type": "code", |
||
| 1624 | "execution_count": null, |
||
| 1625 | "metadata": {}, |
||
| 1626 | "outputs": [ |
||
| 1627 | { |
||
| 1628 | "data": { |
||
| 1629 | "text/html": [ |
||
| 1630 | "<div>\n", |
||
| 1631 | "<style scoped>\n", |
||
| 1632 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1633 | " vertical-align: middle;\n", |
||
| 1634 | " }\n", |
||
| 1635 | "\n", |
||
| 1636 | " .dataframe tbody tr th {\n", |
||
| 1637 | " vertical-align: top;\n", |
||
| 1638 | " }\n", |
||
| 1639 | "\n", |
||
| 1640 | " .dataframe thead th {\n", |
||
| 1641 | " text-align: right;\n", |
||
| 1642 | " }\n", |
||
| 1643 | "</style>\n", |
||
| 1644 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1645 | " <thead>\n", |
||
| 1646 | " <tr style=\"text-align: right;\">\n", |
||
| 1647 | " <th></th>\n", |
||
| 1648 | " <th>#CHROM</th>\n", |
||
| 1649 | " <th>ID</th>\n", |
||
| 1650 | " <th>POS</th>\n", |
||
| 1651 | " <th>A1</th>\n", |
||
| 1652 | " <th>A2</th>\n", |
||
| 1653 | " <th>N</th>\n", |
||
| 1654 | " <th>AF1</th>\n", |
||
| 1655 | " <th>BETA</th>\n", |
||
| 1656 | " <th>SE</th>\n", |
||
| 1657 | " <th>P</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>rs3131962</td>\n", |
||
| 1665 | " <td>756604</td>\n", |
||
| 1666 | " <td>A</td>\n", |
||
| 1667 | " <td>G</td>\n", |
||
| 1668 | " <td>407023</td>\n", |
||
| 1669 | " <td>0.129655</td>\n", |
||
| 1670 | " <td>0.000286</td>\n", |
||
| 1671 | " <td>0.001048</td>\n", |
||
| 1672 | " <td>0.784760</td>\n", |
||
| 1673 | " </tr>\n", |
||
| 1674 | " <tr>\n", |
||
| 1675 | " <th>1</th>\n", |
||
| 1676 | " <td>1</td>\n", |
||
| 1677 | " <td>rs12562034</td>\n", |
||
| 1678 | " <td>768448</td>\n", |
||
| 1679 | " <td>A</td>\n", |
||
| 1680 | " <td>G</td>\n", |
||
| 1681 | " <td>407057</td>\n", |
||
| 1682 | " <td>0.104966</td>\n", |
||
| 1683 | " <td>-0.001491</td>\n", |
||
| 1684 | " <td>0.001147</td>\n", |
||
| 1685 | " <td>0.193592</td>\n", |
||
| 1686 | " </tr>\n", |
||
| 1687 | " <tr>\n", |
||
| 1688 | " <th>2</th>\n", |
||
| 1689 | " <td>1</td>\n", |
||
| 1690 | " <td>rs4040617</td>\n", |
||
| 1691 | " <td>779322</td>\n", |
||
| 1692 | " <td>G</td>\n", |
||
| 1693 | " <td>A</td>\n", |
||
| 1694 | " <td>406623</td>\n", |
||
| 1695 | " <td>0.127520</td>\n", |
||
| 1696 | " <td>0.000108</td>\n", |
||
| 1697 | " <td>0.001056</td>\n", |
||
| 1698 | " <td>0.918404</td>\n", |
||
| 1699 | " </tr>\n", |
||
| 1700 | " <tr>\n", |
||
| 1701 | " <th>3</th>\n", |
||
| 1702 | " <td>1</td>\n", |
||
| 1703 | " <td>rs79373928</td>\n", |
||
| 1704 | " <td>801536</td>\n", |
||
| 1705 | " <td>G</td>\n", |
||
| 1706 | " <td>T</td>\n", |
||
| 1707 | " <td>407517</td>\n", |
||
| 1708 | " <td>0.014884</td>\n", |
||
| 1709 | " <td>0.004382</td>\n", |
||
| 1710 | " <td>0.002904</td>\n", |
||
| 1711 | " <td>0.131349</td>\n", |
||
| 1712 | " </tr>\n", |
||
| 1713 | " <tr>\n", |
||
| 1714 | " <th>4</th>\n", |
||
| 1715 | " <td>1</td>\n", |
||
| 1716 | " <td>rs11240779</td>\n", |
||
| 1717 | " <td>808631</td>\n", |
||
| 1718 | " <td>G</td>\n", |
||
| 1719 | " <td>A</td>\n", |
||
| 1720 | " <td>404493</td>\n", |
||
| 1721 | " <td>0.224886</td>\n", |
||
| 1722 | " <td>-0.001155</td>\n", |
||
| 1723 | " <td>0.000846</td>\n", |
||
| 1724 | " <td>0.172345</td>\n", |
||
| 1725 | " </tr>\n", |
||
| 1726 | " <tr>\n", |
||
| 1727 | " <th>...</th>\n", |
||
| 1728 | " <td>...</td>\n", |
||
| 1729 | " <td>...</td>\n", |
||
| 1730 | " <td>...</td>\n", |
||
| 1731 | " <td>...</td>\n", |
||
| 1732 | " <td>...</td>\n", |
||
| 1733 | " <td>...</td>\n", |
||
| 1734 | " <td>...</td>\n", |
||
| 1735 | " <td>...</td>\n", |
||
| 1736 | " <td>...</td>\n", |
||
| 1737 | " <td>...</td>\n", |
||
| 1738 | " </tr>\n", |
||
| 1739 | " <tr>\n", |
||
| 1740 | " <th>542753</th>\n", |
||
| 1741 | " <td>22</td>\n", |
||
| 1742 | " <td>rs73174435</td>\n", |
||
| 1743 | " <td>51174939</td>\n", |
||
| 1744 | " <td>T</td>\n", |
||
| 1745 | " <td>C</td>\n", |
||
| 1746 | " <td>407201</td>\n", |
||
| 1747 | " <td>0.053846</td>\n", |
||
| 1748 | " <td>-0.001980</td>\n", |
||
| 1749 | " <td>0.001559</td>\n", |
||
| 1750 | " <td>0.203959</td>\n", |
||
| 1751 | " </tr>\n", |
||
| 1752 | " <tr>\n", |
||
| 1753 | " <th>542754</th>\n", |
||
| 1754 | " <td>22</td>\n", |
||
| 1755 | " <td>rs3810648</td>\n", |
||
| 1756 | " <td>51175626</td>\n", |
||
| 1757 | " <td>G</td>\n", |
||
| 1758 | " <td>A</td>\n", |
||
| 1759 | " <td>404901</td>\n", |
||
| 1760 | " <td>0.060979</td>\n", |
||
| 1761 | " <td>0.001922</td>\n", |
||
| 1762 | " <td>0.001474</td>\n", |
||
| 1763 | " <td>0.192116</td>\n", |
||
| 1764 | " </tr>\n", |
||
| 1765 | " <tr>\n", |
||
| 1766 | " <th>542755</th>\n", |
||
| 1767 | " <td>22</td>\n", |
||
| 1768 | " <td>rs5771002</td>\n", |
||
| 1769 | " <td>51183255</td>\n", |
||
| 1770 | " <td>A</td>\n", |
||
| 1771 | " <td>G</td>\n", |
||
| 1772 | " <td>401398</td>\n", |
||
| 1773 | " <td>0.333603</td>\n", |
||
| 1774 | " <td>-0.000165</td>\n", |
||
| 1775 | " <td>0.000751</td>\n", |
||
| 1776 | " <td>0.826494</td>\n", |
||
| 1777 | " </tr>\n", |
||
| 1778 | " <tr>\n", |
||
| 1779 | " <th>542756</th>\n", |
||
| 1780 | " <td>22</td>\n", |
||
| 1781 | " <td>rs3865764</td>\n", |
||
| 1782 | " <td>51185848</td>\n", |
||
| 1783 | " <td>G</td>\n", |
||
| 1784 | " <td>A</td>\n", |
||
| 1785 | " <td>406611</td>\n", |
||
| 1786 | " <td>0.050601</td>\n", |
||
| 1787 | " <td>-0.001311</td>\n", |
||
| 1788 | " <td>0.001605</td>\n", |
||
| 1789 | " <td>0.413994</td>\n", |
||
| 1790 | " </tr>\n", |
||
| 1791 | " <tr>\n", |
||
| 1792 | " <th>542757</th>\n", |
||
| 1793 | " <td>22</td>\n", |
||
| 1794 | " <td>rs142680588</td>\n", |
||
| 1795 | " <td>51193629</td>\n", |
||
| 1796 | " <td>G</td>\n", |
||
| 1797 | " <td>A</td>\n", |
||
| 1798 | " <td>407108</td>\n", |
||
| 1799 | " <td>0.075912</td>\n", |
||
| 1800 | " <td>-0.002861</td>\n", |
||
| 1801 | " <td>0.001329</td>\n", |
||
| 1802 | " <td>0.031362</td>\n", |
||
| 1803 | " </tr>\n", |
||
| 1804 | " </tbody>\n", |
||
| 1805 | "</table>\n", |
||
| 1806 | "<p>542758 rows × 10 columns</p>\n", |
||
| 1807 | "</div>" |
||
| 1808 | ], |
||
| 1809 | "text/plain": [ |
||
| 1810 | " #CHROM ID POS A1 A2 N AF1 BETA \\\n", |
||
| 1811 | "0 1 rs3131962 756604 A G 407023 0.129655 0.000286 \n", |
||
| 1812 | "1 1 rs12562034 768448 A G 407057 0.104966 -0.001491 \n", |
||
| 1813 | "2 1 rs4040617 779322 G A 406623 0.127520 0.000108 \n", |
||
| 1814 | "3 1 rs79373928 801536 G T 407517 0.014884 0.004382 \n", |
||
| 1815 | "4 1 rs11240779 808631 G A 404493 0.224886 -0.001155 \n", |
||
| 1816 | "... ... ... ... .. .. ... ... ... \n", |
||
| 1817 | "542753 22 rs73174435 51174939 T C 407201 0.053846 -0.001980 \n", |
||
| 1818 | "542754 22 rs3810648 51175626 G A 404901 0.060979 0.001922 \n", |
||
| 1819 | "542755 22 rs5771002 51183255 A G 401398 0.333603 -0.000165 \n", |
||
| 1820 | "542756 22 rs3865764 51185848 G A 406611 0.050601 -0.001311 \n", |
||
| 1821 | "542757 22 rs142680588 51193629 G A 407108 0.075912 -0.002861 \n", |
||
| 1822 | "\n", |
||
| 1823 | " SE P \n", |
||
| 1824 | "0 0.001048 0.784760 \n", |
||
| 1825 | "1 0.001147 0.193592 \n", |
||
| 1826 | "2 0.001056 0.918404 \n", |
||
| 1827 | "3 0.002904 0.131349 \n", |
||
| 1828 | "4 0.000846 0.172345 \n", |
||
| 1829 | "... ... ... \n", |
||
| 1830 | "542753 0.001559 0.203959 \n", |
||
| 1831 | "542754 0.001474 0.192116 \n", |
||
| 1832 | "542755 0.000751 0.826494 \n", |
||
| 1833 | "542756 0.001605 0.413994 \n", |
||
| 1834 | "542757 0.001329 0.031362 \n", |
||
| 1835 | "\n", |
||
| 1836 | "[542758 rows x 10 columns]" |
||
| 1837 | ] |
||
| 1838 | }, |
||
| 1839 | "execution_count": 7, |
||
| 1840 | "metadata": {}, |
||
| 1841 | "output_type": "execute_result" |
||
| 1842 | } |
||
| 1843 | ], |
||
| 1844 | "source": [ |
||
| 1845 | "data.load_full_gwas(pheno = 'body_BALDING1')\n", |
||
| 1846 | "data.lr_uni" |
||
| 1847 | ] |
||
| 1848 | }, |
||
| 1849 | { |
||
| 1850 | "cell_type": "markdown", |
||
| 1851 | "metadata": {}, |
||
| 1852 | "source": [ |
||
| 1853 | "This is the basic KGWAS interface! Check out the other notebooks for other capabilities of KGWAS!" |
||
| 1854 | ] |
||
| 1855 | } |
||
| 1856 | ], |
||
| 1857 | "metadata": { |
||
| 1858 | "kernelspec": { |
||
| 1859 | "display_name": "a100_env", |
||
| 1860 | "language": "python", |
||
| 1861 | "name": "python3" |
||
| 1862 | }, |
||
| 1863 | "language_info": { |
||
| 1864 | "codemirror_mode": { |
||
| 1865 | "name": "ipython", |
||
| 1866 | "version": 3 |
||
| 1867 | }, |
||
| 1868 | "file_extension": ".py", |
||
| 1869 | "mimetype": "text/x-python", |
||
| 1870 | "name": "python", |
||
| 1871 | "nbconvert_exporter": "python", |
||
| 1872 | "pygments_lexer": "ipython3", |
||
| 1873 | "version": "3.8.0" |
||
| 1874 | } |
||
| 1875 | }, |
||
| 1876 | "nbformat": 4, |
||
| 1877 | "nbformat_minor": 2 |
||
| 1878 | } |