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Updated with v1.0.10 output
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@francois-a
francois-a committed Aug 24, 2024
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104 changes: 52 additions & 52 deletions example/tensorqtl_examples.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"torch: 2.1.2+cu121 (CUDA 12.1), device: cuda\n",
"pandas 2.2.1\n"
"torch: 2.4.0+cu121 (CUDA 12.1), device: cuda\n",
"pandas 2.2.2\n"
]
}
],
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" * checking phenotypes: 301/301\n",
" * computing permutations\n",
" processing phenotype 301/301\n",
" Time elapsed: 0.36 min\n",
" Time elapsed: 0.31 min\n",
"done.\n",
"Computing q-values\n",
" * Number of phenotypes tested: 301\n",
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" <tr>\n",
" <th>ENSG00000263006.6</th>\n",
" <td>6120</td>\n",
" <td>1.038813</td>\n",
" <td>1138.436646</td>\n",
" <td>374.660431</td>\n",
" <td>8.220932e-40</td>\n",
" <td>1.038811</td>\n",
" <td>1138.434082</td>\n",
" <td>374.660400</td>\n",
" <td>8.220950e-40</td>\n",
" <td>chr18_112535_G_A_b38</td>\n",
" <td>3470</td>\n",
" <td>3470</td>\n",
" <td>212</td>\n",
" <td>251</td>\n",
" <td>0.282022</td>\n",
" <td>4.050327e-44</td>\n",
" <td>4.050344e-44</td>\n",
" <td>0.726425</td>\n",
" <td>0.046171</td>\n",
" <td>0.000100</td>\n",
" <td>3.677249e-38</td>\n",
" <td>2.696649e-37</td>\n",
" <td>3.677735e-38</td>\n",
" <td>2.697006e-37</td>\n",
" <td>0.000141</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ENSG00000101557.14</th>\n",
" <td>6355</td>\n",
" <td>1.032238</td>\n",
" <td>1076.303711</td>\n",
" <td>1.032237</td>\n",
" <td>1076.303223</td>\n",
" <td>370.176422</td>\n",
" <td>5.632804e-11</td>\n",
" <td>5.632806e-11</td>\n",
" <td>chr18_210698_T_C_b38</td>\n",
" <td>52315</td>\n",
" <td>52315</td>\n",
" <td>192</td>\n",
" <td>222</td>\n",
" <td>0.249438</td>\n",
" <td>3.505407e-12</td>\n",
" <td>3.505411e-12</td>\n",
" <td>-0.191712</td>\n",
" <td>0.026749</td>\n",
" <td>0.000100</td>\n",
" <td>3.498881e-08</td>\n",
" <td>3.563675e-08</td>\n",
" <td>3.498951e-08</td>\n",
" <td>3.563747e-08</td>\n",
" <td>0.000146</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ENSG00000079134.11</th>\n",
" <td>6921</td>\n",
" <td>1.047218</td>\n",
" <td>1155.657959</td>\n",
" <td>1.047219</td>\n",
" <td>1155.660156</td>\n",
" <td>370.356049</td>\n",
" <td>3.888736e-08</td>\n",
" <td>3.888738e-08</td>\n",
" <td>chr18_243547_T_A_b38</td>\n",
" <td>-24503</td>\n",
" <td>-24503</td>\n",
Expand All @@ -409,49 +409,49 @@
" <td>-0.122720</td>\n",
" <td>0.020602</td>\n",
" <td>0.000100</td>\n",
" <td>2.743990e-05</td>\n",
" <td>1.916437e-05</td>\n",
" <td>2.743975e-05</td>\n",
" <td>1.916427e-05</td>\n",
" <td>0.000141</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ENSG00000263884.1</th>\n",
" <td>6921</td>\n",
" <td>1.039806</td>\n",
" <td>1152.499878</td>\n",
" <td>369.873535</td>\n",
" <td>7.681883e-04</td>\n",
" <td>1152.501587</td>\n",
" <td>369.873505</td>\n",
" <td>7.681884e-04</td>\n",
" <td>chr18_584440_G_C_b38</td>\n",
" <td>316292</td>\n",
" <td>316292</td>\n",
" <td>81</td>\n",
" <td>88</td>\n",
" <td>0.098876</td>\n",
" <td>3.540397e-04</td>\n",
" <td>3.540399e-04</td>\n",
" <td>-0.330811</td>\n",
" <td>0.091845</td>\n",
" <td>0.574843</td>\n",
" <td>5.695495e-01</td>\n",
" <td>1.577697e-01</td>\n",
" <td>5.695498e-01</td>\n",
" <td>1.577698e-01</td>\n",
" <td>0.000139</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ENSG00000158270.11</th>\n",
" <td>8134</td>\n",
" <td>1.054919</td>\n",
" <td>1277.927002</td>\n",
" <td>369.469055</td>\n",
" <td>2.516530e-09</td>\n",
" <td>1277.927246</td>\n",
" <td>369.469086</td>\n",
" <td>2.516529e-09</td>\n",
" <td>chr18_519222_C_T_b38</td>\n",
" <td>18500</td>\n",
" <td>18500</td>\n",
" <td>108</td>\n",
" <td>115</td>\n",
" <td>0.129213</td>\n",
" <td>2.409714e-10</td>\n",
" <td>2.409717e-10</td>\n",
" <td>-0.388277</td>\n",
" <td>0.059808</td>\n",
" <td>0.000100</td>\n",
" <td>1.567347e-06</td>\n",
" <td>1.567348e-06</td>\n",
" <td>1.321136e-06</td>\n",
" <td>0.000130</td>\n",
" </tr>\n",
Expand All @@ -462,19 +462,19 @@
"text/plain": [
" num_var beta_shape1 beta_shape2 true_df \\\n",
"phenotype_id \n",
"ENSG00000263006.6 6120 1.038813 1138.436646 374.660431 \n",
"ENSG00000101557.14 6355 1.032238 1076.303711 370.176422 \n",
"ENSG00000079134.11 6921 1.047218 1155.657959 370.356049 \n",
"ENSG00000263884.1 6921 1.039806 1152.499878 369.873535 \n",
"ENSG00000158270.11 8134 1.054919 1277.927002 369.469055 \n",
"ENSG00000263006.6 6120 1.038811 1138.434082 374.660400 \n",
"ENSG00000101557.14 6355 1.032237 1076.303223 370.176422 \n",
"ENSG00000079134.11 6921 1.047219 1155.660156 370.356049 \n",
"ENSG00000263884.1 6921 1.039806 1152.501587 369.873505 \n",
"ENSG00000158270.11 8134 1.054919 1277.927246 369.469086 \n",
"\n",
" pval_true_df variant_id start_distance \\\n",
"phenotype_id \n",
"ENSG00000263006.6 8.220932e-40 chr18_112535_G_A_b38 3470 \n",
"ENSG00000101557.14 5.632804e-11 chr18_210698_T_C_b38 52315 \n",
"ENSG00000079134.11 3.888736e-08 chr18_243547_T_A_b38 -24503 \n",
"ENSG00000263884.1 7.681883e-04 chr18_584440_G_C_b38 316292 \n",
"ENSG00000158270.11 2.516530e-09 chr18_519222_C_T_b38 18500 \n",
"ENSG00000263006.6 8.220950e-40 chr18_112535_G_A_b38 3470 \n",
"ENSG00000101557.14 5.632806e-11 chr18_210698_T_C_b38 52315 \n",
"ENSG00000079134.11 3.888738e-08 chr18_243547_T_A_b38 -24503 \n",
"ENSG00000263884.1 7.681884e-04 chr18_584440_G_C_b38 316292 \n",
"ENSG00000158270.11 2.516529e-09 chr18_519222_C_T_b38 18500 \n",
"\n",
" end_distance ma_samples ma_count af \\\n",
"phenotype_id \n",
Expand All @@ -486,18 +486,18 @@
"\n",
" pval_nominal slope slope_se pval_perm pval_beta \\\n",
"phenotype_id \n",
"ENSG00000263006.6 4.050327e-44 0.726425 0.046171 0.000100 3.677249e-38 \n",
"ENSG00000101557.14 3.505407e-12 -0.191712 0.026749 0.000100 3.498881e-08 \n",
"ENSG00000079134.11 5.473709e-09 -0.122720 0.020602 0.000100 2.743990e-05 \n",
"ENSG00000263884.1 3.540397e-04 -0.330811 0.091845 0.574843 5.695495e-01 \n",
"ENSG00000158270.11 2.409714e-10 -0.388277 0.059808 0.000100 1.567347e-06 \n",
"ENSG00000263006.6 4.050344e-44 0.726425 0.046171 0.000100 3.677735e-38 \n",
"ENSG00000101557.14 3.505411e-12 -0.191712 0.026749 0.000100 3.498951e-08 \n",
"ENSG00000079134.11 5.473709e-09 -0.122720 0.020602 0.000100 2.743975e-05 \n",
"ENSG00000263884.1 3.540399e-04 -0.330811 0.091845 0.574843 5.695498e-01 \n",
"ENSG00000158270.11 2.409717e-10 -0.388277 0.059808 0.000100 1.567348e-06 \n",
"\n",
" qval pval_nominal_threshold \n",
"phenotype_id \n",
"ENSG00000263006.6 2.696649e-37 0.000141 \n",
"ENSG00000101557.14 3.563675e-08 0.000146 \n",
"ENSG00000079134.11 1.916437e-05 0.000141 \n",
"ENSG00000263884.1 1.577697e-01 0.000139 \n",
"ENSG00000263006.6 2.697006e-37 0.000141 \n",
"ENSG00000101557.14 3.563747e-08 0.000146 \n",
"ENSG00000079134.11 1.916427e-05 0.000141 \n",
"ENSG00000263884.1 1.577698e-01 0.000139 \n",
"ENSG00000158270.11 1.321136e-06 0.000130 "
]
},
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.7"
"version": "3.11.9"
}
},
"nbformat": 4,
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