diff --git a/example/tensorqtl_examples.ipynb b/example/tensorqtl_examples.ipynb index 12f9918..1c80cae 100644 --- a/example/tensorqtl_examples.ipynb +++ b/example/tensorqtl_examples.ipynb @@ -27,8 +27,8 @@ "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" ] } ], @@ -257,7 +257,7 @@ " * 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", @@ -353,52 +353,52 @@ " \n", " ENSG00000263006.6\n", " 6120\n", - " 1.038813\n", - " 1138.436646\n", - " 374.660431\n", - " 8.220932e-40\n", + " 1.038811\n", + " 1138.434082\n", + " 374.660400\n", + " 8.220950e-40\n", " chr18_112535_G_A_b38\n", " 3470\n", " 3470\n", " 212\n", " 251\n", " 0.282022\n", - " 4.050327e-44\n", + " 4.050344e-44\n", " 0.726425\n", " 0.046171\n", " 0.000100\n", - " 3.677249e-38\n", - " 2.696649e-37\n", + " 3.677735e-38\n", + " 2.697006e-37\n", " 0.000141\n", " \n", " \n", " ENSG00000101557.14\n", " 6355\n", - " 1.032238\n", - " 1076.303711\n", + " 1.032237\n", + " 1076.303223\n", " 370.176422\n", - " 5.632804e-11\n", + " 5.632806e-11\n", " chr18_210698_T_C_b38\n", " 52315\n", " 52315\n", " 192\n", " 222\n", " 0.249438\n", - " 3.505407e-12\n", + " 3.505411e-12\n", " -0.191712\n", " 0.026749\n", " 0.000100\n", - " 3.498881e-08\n", - " 3.563675e-08\n", + " 3.498951e-08\n", + " 3.563747e-08\n", " 0.000146\n", " \n", " \n", " ENSG00000079134.11\n", " 6921\n", - " 1.047218\n", - " 1155.657959\n", + " 1.047219\n", + " 1155.660156\n", " 370.356049\n", - " 3.888736e-08\n", + " 3.888738e-08\n", " chr18_243547_T_A_b38\n", " -24503\n", " -24503\n", @@ -409,49 +409,49 @@ " -0.122720\n", " 0.020602\n", " 0.000100\n", - " 2.743990e-05\n", - " 1.916437e-05\n", + " 2.743975e-05\n", + " 1.916427e-05\n", " 0.000141\n", " \n", " \n", " ENSG00000263884.1\n", " 6921\n", " 1.039806\n", - " 1152.499878\n", - " 369.873535\n", - " 7.681883e-04\n", + " 1152.501587\n", + " 369.873505\n", + " 7.681884e-04\n", " chr18_584440_G_C_b38\n", " 316292\n", " 316292\n", " 81\n", " 88\n", " 0.098876\n", - " 3.540397e-04\n", + " 3.540399e-04\n", " -0.330811\n", " 0.091845\n", " 0.574843\n", - " 5.695495e-01\n", - " 1.577697e-01\n", + " 5.695498e-01\n", + " 1.577698e-01\n", " 0.000139\n", " \n", " \n", " ENSG00000158270.11\n", " 8134\n", " 1.054919\n", - " 1277.927002\n", - " 369.469055\n", - " 2.516530e-09\n", + " 1277.927246\n", + " 369.469086\n", + " 2.516529e-09\n", " chr18_519222_C_T_b38\n", " 18500\n", " 18500\n", " 108\n", " 115\n", " 0.129213\n", - " 2.409714e-10\n", + " 2.409717e-10\n", " -0.388277\n", " 0.059808\n", " 0.000100\n", - " 1.567347e-06\n", + " 1.567348e-06\n", " 1.321136e-06\n", " 0.000130\n", " \n", @@ -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", @@ -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 " ] }, @@ -688,7 +688,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.7" + "version": "3.11.9" } }, "nbformat": 4,