diff --git a/nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.ipynb b/nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.ipynb index 5f63a11c..b785acc8 100644 --- a/nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.ipynb +++ b/nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.ipynb @@ -5,10 +5,10 @@ "id": "e9773a95-e8fd-4963-87a5-0c92299434d5", "metadata": { "papermill": { - "duration": 0.047408, - "end_time": "2022-01-21T05:24:19.991077", + "duration": 0.006476, + "end_time": "2023-09-07T01:00:39.583786", "exception": false, - "start_time": "2022-01-21T05:24:19.943669", + "start_time": "2023-09-07T01:00:39.577310", "status": "completed" }, "tags": [] @@ -22,10 +22,10 @@ "id": "57f34c74-404d-4776-b547-e6acb2df75d7", "metadata": { "papermill": { - "duration": 0.012965, - "end_time": "2022-01-21T05:24:20.020631", + "duration": 0.006028, + "end_time": "2023-09-07T01:00:39.599713", "exception": false, - "start_time": "2022-01-21T05:24:20.007666", + "start_time": "2023-09-07T01:00:39.593685", "status": "completed" }, "tags": [] @@ -42,10 +42,10 @@ "id": "1d8fae6b-e623-46a6-aff6-d7849163c820", "metadata": { "papermill": { - "duration": 0.01299, - "end_time": "2022-01-21T05:24:20.046748", + "duration": 0.002637, + "end_time": "2023-09-07T01:00:39.608531", "exception": false, - "start_time": "2022-01-21T05:24:20.033758", + "start_time": "2023-09-07T01:00:39.605894", "status": "completed" }, "tags": [] @@ -60,16 +60,16 @@ "id": "76729f0e-f742-495b-b676-d9d7b1539e10", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.080474Z", - "iopub.status.busy": "2022-01-21T05:24:20.080013Z", - "iopub.status.idle": "2022-01-21T05:24:20.526977Z", - "shell.execute_reply": "2022-01-21T05:24:20.526453Z" + "iopub.execute_input": "2023-09-07T01:00:39.613281Z", + "iopub.status.busy": "2023-09-07T01:00:39.612955Z", + "iopub.status.idle": "2023-09-07T01:00:39.837995Z", + "shell.execute_reply": "2023-09-07T01:00:39.837698Z" }, "papermill": { - "duration": 0.466683, - "end_time": "2022-01-21T05:24:20.527087", + "duration": 0.228116, + "end_time": "2023-09-07T01:00:39.838874", "exception": false, - "start_time": "2022-01-21T05:24:20.060404", + "start_time": "2023-09-07T01:00:39.610758", "status": "completed" }, "tags": [] @@ -91,10 +91,10 @@ "id": "a6c3a546-9a49-45e7-9f17-fbdb5af4bfb6", "metadata": { "papermill": { - "duration": 0.013452, - "end_time": "2022-01-21T05:24:20.554436", + "duration": 0.009804, + "end_time": "2023-09-07T01:00:39.850195", "exception": false, - "start_time": "2022-01-21T05:24:20.540984", + "start_time": "2023-09-07T01:00:39.840391", "status": "completed" }, "tags": [] @@ -109,16 +109,16 @@ "id": "56ff94d3-a230-4028-a71d-518ac109209b", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.584643Z", - "iopub.status.busy": "2022-01-21T05:24:20.584179Z", - "iopub.status.idle": "2022-01-21T05:24:20.585609Z", - "shell.execute_reply": "2022-01-21T05:24:20.585960Z" + "iopub.execute_input": "2023-09-07T01:00:39.855368Z", + "iopub.status.busy": "2023-09-07T01:00:39.855269Z", + "iopub.status.idle": "2023-09-07T01:00:39.857036Z", + "shell.execute_reply": "2023-09-07T01:00:39.856746Z" }, "papermill": { - "duration": 0.018351, - "end_time": "2022-01-21T05:24:20.586068", + "duration": 0.004665, + "end_time": "2023-09-07T01:00:39.857699", "exception": false, - "start_time": "2022-01-21T05:24:20.567717", + "start_time": "2023-09-07T01:00:39.853034", "status": "completed" }, "tags": [] @@ -134,16 +134,16 @@ "id": "ac2eaa49-c49e-4f3c-83c5-4f8c321d25a7", "metadata": { "execution": { - "iopub.execute_input": "2022-05-24T14:46:59.207591Z", - "iopub.status.busy": "2022-05-24T14:46:59.207409Z", - "iopub.status.idle": "2022-05-24T14:46:59.210688Z", - "shell.execute_reply": "2022-05-24T14:46:59.210092Z" + "iopub.execute_input": "2023-09-07T01:00:39.862108Z", + "iopub.status.busy": "2023-09-07T01:00:39.862020Z", + "iopub.status.idle": "2023-09-07T01:00:39.863857Z", + "shell.execute_reply": "2023-09-07T01:00:39.863653Z" }, "papermill": { - "duration": 0.010126, - "end_time": "2022-05-24T14:46:59.212259", + "duration": 0.004714, + "end_time": "2023-09-07T01:00:39.864436", "exception": false, - "start_time": "2022-05-24T14:46:59.202133", + "start_time": "2023-09-07T01:00:39.859722", "status": "completed" }, "tags": [] @@ -162,20 +162,20 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "id": "8baf4209-ba56-4e3d-b60f-6ce2bb686159", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.621121Z", - "iopub.status.busy": "2022-01-21T05:24:20.614967Z", - "iopub.status.idle": "2022-01-21T05:24:20.624112Z", - "shell.execute_reply": "2022-01-21T05:24:20.623691Z" + "iopub.execute_input": "2023-09-07T01:00:39.868961Z", + "iopub.status.busy": "2023-09-07T01:00:39.868839Z", + "iopub.status.idle": "2023-09-07T01:00:39.874105Z", + "shell.execute_reply": "2023-09-07T01:00:39.873784Z" }, "papermill": { - "duration": 0.024352, - "end_time": "2022-01-21T05:24:20.624205", + "duration": 0.008499, + "end_time": "2023-09-07T01:00:39.874847", "exception": false, - "start_time": "2022-01-21T05:24:20.599853", + "start_time": "2023-09-07T01:00:39.866348", "status": "completed" }, "tags": [] @@ -200,20 +200,20 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "id": "21a3e349-9a09-4d24-89e3-915fdbf08a81", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.654986Z", - "iopub.status.busy": "2022-01-21T05:24:20.654541Z", - "iopub.status.idle": "2022-01-21T05:24:20.656487Z", - "shell.execute_reply": "2022-01-21T05:24:20.656848Z" + "iopub.execute_input": "2023-09-07T01:00:39.879634Z", + "iopub.status.busy": "2023-09-07T01:00:39.879359Z", + "iopub.status.idle": "2023-09-07T01:00:39.881411Z", + "shell.execute_reply": "2023-09-07T01:00:39.881200Z" }, "papermill": { - "duration": 0.018901, - "end_time": "2022-01-21T05:24:20.656957", + "duration": 0.005054, + "end_time": "2023-09-07T01:00:39.881911", "exception": false, - "start_time": "2022-01-21T05:24:20.638056", + "start_time": "2023-09-07T01:00:39.876857", "status": "completed" }, "tags": [] @@ -228,10 +228,10 @@ "id": "b0afcba9-5847-414e-b448-f0cd08ecd8ce", "metadata": { "papermill": { - "duration": 0.01368, - "end_time": "2022-01-21T05:24:20.684808", + "duration": 0.001818, + "end_time": "2023-09-07T01:00:39.885488", "exception": false, - "start_time": "2022-01-21T05:24:20.671128", + "start_time": "2023-09-07T01:00:39.883670", "status": "completed" }, "tags": [] @@ -242,20 +242,20 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "id": "35760114-8560-4a0e-ad4f-2bee9104c63d", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.715608Z", - "iopub.status.busy": "2022-01-21T05:24:20.713691Z", - "iopub.status.idle": "2022-01-21T05:24:20.718185Z", - "shell.execute_reply": "2022-01-21T05:24:20.717796Z" + "iopub.execute_input": "2023-09-07T01:00:39.889264Z", + "iopub.status.busy": "2023-09-07T01:00:39.889118Z", + "iopub.status.idle": "2023-09-07T01:00:39.891521Z", + "shell.execute_reply": "2023-09-07T01:00:39.891237Z" }, "papermill": { - "duration": 0.019837, - "end_time": "2022-01-21T05:24:20.718280", + "duration": 0.004744, + "end_time": "2023-09-07T01:00:39.891993", "exception": false, - "start_time": "2022-01-21T05:24:20.698443", + "start_time": "2023-09-07T01:00:39.887249", "status": "completed" }, "tags": [] @@ -280,20 +280,20 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "id": "f1418e81-4e77-4f67-b5ed-b29b797e31a0", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.751658Z", - "iopub.status.busy": "2022-01-21T05:24:20.751171Z", - "iopub.status.idle": "2022-01-21T05:24:20.753878Z", - "shell.execute_reply": "2022-01-21T05:24:20.753442Z" + "iopub.execute_input": "2023-09-07T01:00:39.895292Z", + "iopub.status.busy": "2023-09-07T01:00:39.895134Z", + "iopub.status.idle": "2023-09-07T01:00:39.897316Z", + "shell.execute_reply": "2023-09-07T01:00:39.897146Z" }, "papermill": { - "duration": 0.021021, - "end_time": "2022-01-21T05:24:20.753970", + "duration": 0.004236, + "end_time": "2023-09-07T01:00:39.897711", "exception": false, - "start_time": "2022-01-21T05:24:20.732949", + "start_time": "2023-09-07T01:00:39.893475", "status": "completed" }, "tags": [] @@ -320,10 +320,10 @@ "id": "5fdf8df6-eba0-4cf5-979c-3acd56a5ef3c", "metadata": { "papermill": { - "duration": 0.014277, - "end_time": "2022-01-21T05:24:20.782880", + "duration": 0.001252, + "end_time": "2023-09-07T01:00:39.900304", "exception": false, - "start_time": "2022-01-21T05:24:20.768603", + "start_time": "2023-09-07T01:00:39.899052", "status": "completed" }, "tags": [] @@ -334,20 +334,45 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "id": "596d25ed-4120-4bef-8984-a91ae6529ab5", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.815780Z", - "iopub.status.busy": "2022-01-21T05:24:20.815343Z", - "iopub.status.idle": "2022-01-21T05:24:20.820224Z", - "shell.execute_reply": "2022-01-21T05:24:20.820574Z" + "iopub.execute_input": "2023-09-07T01:00:39.903380Z", + "iopub.status.busy": "2023-09-07T01:00:39.903236Z", + "iopub.status.idle": "2023-09-07T01:00:39.904825Z", + "shell.execute_reply": "2023-09-07T01:00:39.904647Z" + }, + "papermill": { + "duration": 0.003603, + "end_time": "2023-09-07T01:00:39.905221", + "exception": false, + "start_time": "2023-09-07T01:00:39.901618", + "status": "completed" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "tissue_in_file_names = [f\"_data_{simplify_string(t.lower())}-\" for t in TISSUES]" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "cd78a8c5", + "metadata": { + "execution": { + "iopub.execute_input": "2023-09-07T01:00:39.908339Z", + "iopub.status.busy": "2023-09-07T01:00:39.908201Z", + "iopub.status.idle": "2023-09-07T01:00:39.911606Z", + "shell.execute_reply": "2023-09-07T01:00:39.911436Z" }, "papermill": { - "duration": 0.023283, - "end_time": "2022-01-21T05:24:20.820688", + "duration": 0.00542, + "end_time": "2023-09-07T01:00:39.912024", "exception": false, - "start_time": "2022-01-21T05:24:20.797405", + "start_time": "2023-09-07T01:00:39.906604", "status": "completed" }, "tags": [] @@ -356,7 +381,7 @@ { "data": { "text/plain": [ - "54" + "1" ] }, "metadata": {}, @@ -365,29 +390,13 @@ { "data": { "text/plain": [ - "[PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_adipose_subcutaneous-var_pc_log2.pkl'),\n", - " PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_adipose_visceral_omentum-var_pc_log2.pkl'),\n", - " PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_adrenal_gland-var_pc_log2.pkl'),\n", - " PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_artery_aorta-var_pc_log2.pkl'),\n", - " PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_artery_coronary-var_pc_log2.pkl')]" + "[PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_whole_blood-var_pc_log2.pkl')]" ] }, "metadata": {}, "output_type": "display_data" } ], - "source": [ - "tissue_in_file_names = [f\"_data_{simplify_string(t.lower())}-\" for t in TISSUES]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "cd78a8c5", - "metadata": { - "tags": [] - }, - "outputs": [], "source": [ "input_files = sorted(list(INPUT_DIR.glob(f\"*-{GENE_SELECTION_STRATEGY}.pkl\")))\n", "input_files = [\n", @@ -404,10 +413,10 @@ "id": "081da632-fd12-462a-9ae1-c0ceccf1bb5d", "metadata": { "papermill": { - "duration": 0.015229, - "end_time": "2022-01-21T05:24:20.851314", + "duration": 0.001359, + "end_time": "2023-09-07T01:00:39.914795", "exception": false, - "start_time": "2022-01-21T05:24:20.836085", + "start_time": "2023-09-07T01:00:39.913436", "status": "completed" }, "tags": [] @@ -421,10 +430,10 @@ "id": "37137fff-2d3a-43d8-9bd5-d7c3284a97f5", "metadata": { "papermill": { - "duration": 0.014906, - "end_time": "2022-01-21T05:24:20.881327", + "duration": 0.001323, + "end_time": "2023-09-07T01:00:39.917500", "exception": false, - "start_time": "2022-01-21T05:24:20.866421", + "start_time": "2023-09-07T01:00:39.916177", "status": "completed" }, "tags": [] @@ -435,20 +444,20 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 10, "id": "5dd40707-759f-4bf9-b8cc-84811b2dfe53", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.915057Z", - "iopub.status.busy": "2022-01-21T05:24:20.914461Z", - "iopub.status.idle": "2022-01-21T05:24:20.928410Z", - "shell.execute_reply": "2022-01-21T05:24:20.927945Z" + "iopub.execute_input": "2023-09-07T01:00:39.920791Z", + "iopub.status.busy": "2023-09-07T01:00:39.920650Z", + "iopub.status.idle": "2023-09-07T01:00:39.930929Z", + "shell.execute_reply": "2023-09-07T01:00:39.930780Z" }, "papermill": { - "duration": 0.032039, - "end_time": "2022-01-21T05:24:20.928505", + "duration": 0.012393, + "end_time": "2023-09-07T01:00:39.931365", "exception": false, - "start_time": "2022-01-21T05:24:20.896466", + "start_time": "2023-09-07T01:00:39.918972", "status": "completed" }, "tags": [] @@ -457,7 +466,7 @@ { "data": { "text/plain": [ - "PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_adipose_subcutaneous-var_pc_log2.pkl')" + "PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_whole_blood-var_pc_log2.pkl')" ] }, "metadata": {}, @@ -471,20 +480,20 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 11, "id": "e8acd036-93f7-46c0-a1ee-8da0c2c24790", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:20.964032Z", - "iopub.status.busy": "2022-01-21T05:24:20.963456Z", - "iopub.status.idle": "2022-01-21T05:24:20.965961Z", - "shell.execute_reply": "2022-01-21T05:24:20.966363Z" + "iopub.execute_input": "2023-09-07T01:00:39.934555Z", + "iopub.status.busy": "2023-09-07T01:00:39.934505Z", + "iopub.status.idle": "2023-09-07T01:00:39.936105Z", + "shell.execute_reply": "2023-09-07T01:00:39.935983Z" }, "papermill": { - "duration": 0.02175, - "end_time": "2022-01-21T05:24:20.966486", + "duration": 0.003621, + "end_time": "2023-09-07T01:00:39.936501", "exception": false, - "start_time": "2022-01-21T05:24:20.944736", + "start_time": "2023-09-07T01:00:39.932880", "status": "completed" }, "tags": [] @@ -493,10 +502,10 @@ { "data": { "text/plain": [ - "(500, 663)" + "(500, 755)" ] }, - "execution_count": 9, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -507,20 +516,20 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 12, "id": "111e360b-dbe4-4b69-9029-7b7669eb5ddc", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:21.004121Z", - "iopub.status.busy": "2022-01-21T05:24:21.003631Z", - "iopub.status.idle": "2022-01-21T05:24:21.022339Z", - "shell.execute_reply": "2022-01-21T05:24:21.021901Z" + "iopub.execute_input": "2023-09-07T01:00:39.939756Z", + "iopub.status.busy": "2023-09-07T01:00:39.939686Z", + "iopub.status.idle": "2023-09-07T01:00:39.950161Z", + "shell.execute_reply": "2023-09-07T01:00:39.949953Z" }, "papermill": { - "duration": 0.039109, - "end_time": "2022-01-21T05:24:21.022431", + "duration": 0.012763, + "end_time": "2023-09-07T01:00:39.950777", "exception": false, - "start_time": "2022-01-21T05:24:20.983322", + "start_time": "2023-09-07T01:00:39.938014", "status": "completed" }, "tags": [] @@ -547,27 +556,27 @@ " \n", " \n", " \n", - " GTEX-1117F-0226-SM-5GZZ7\n", - " GTEX-111CU-1826-SM-5GZYN\n", - " GTEX-111FC-0226-SM-5N9B8\n", - " GTEX-111VG-2326-SM-5N9BK\n", - " GTEX-111YS-2426-SM-5GZZQ\n", - " GTEX-1122O-2026-SM-9YFMG\n", - " GTEX-1128S-2126-SM-5H12U\n", - " GTEX-113IC-0226-SM-5HL5C\n", - " GTEX-117YX-2226-SM-5EGJJ\n", - " GTEX-11DXW-0326-SM-5H11W\n", + " GTEX-111YS-0006-SM-5NQBE\n", + " GTEX-1122O-0005-SM-5O99J\n", + " GTEX-1128S-0005-SM-5P9HI\n", + " GTEX-113IC-0006-SM-5NQ9C\n", + " GTEX-113JC-0006-SM-5O997\n", + " GTEX-117XS-0005-SM-5PNU6\n", + " GTEX-117YW-0005-SM-5NQ8Z\n", + " GTEX-1192W-0005-SM-5NQBQ\n", + " GTEX-1192X-0005-SM-5NQC3\n", + " GTEX-11DXW-0006-SM-5NQ7Y\n", " ...\n", - " GTEX-ZXES-2026-SM-5NQ6R\n", - " GTEX-ZXG5-0226-SM-59HJI\n", - " GTEX-ZYFC-0326-SM-5NQ7H\n", - " GTEX-ZYFD-0226-SM-5NQ86\n", - " GTEX-ZYT6-0326-SM-7LG5R\n", - " GTEX-ZYVF-0226-SM-5GIEG\n", - " GTEX-ZYW4-0226-SM-5E44M\n", - " GTEX-ZYY3-0226-SM-5E45M\n", - " GTEX-ZZ64-1626-SM-5E43W\n", - " GTEX-ZZPU-2726-SM-5NQ8O\n", + " GTEX-ZVE2-0006-SM-51MRW\n", + " GTEX-ZVP2-0005-SM-51MRK\n", + " GTEX-ZVT2-0005-SM-57WBW\n", + " GTEX-ZVT3-0006-SM-51MT9\n", + " GTEX-ZVT4-0006-SM-57WB8\n", + " GTEX-ZVTK-0006-SM-57WBK\n", + " GTEX-ZVZP-0006-SM-51MSW\n", + " GTEX-ZVZQ-0006-SM-51MR8\n", + " GTEX-ZXES-0005-SM-57WCB\n", + " GTEX-ZXG5-0005-SM-57WCN\n", " \n", " \n", " gene_ens_id\n", @@ -596,215 +605,215 @@ " \n", " \n", " \n", - " ENSG00000129824.15\n", - " 0.9301\n", - " 270.4000\n", - " 345.8000\n", - " 242.20\n", - " 180.800\n", - " 0.1904\n", - " 0.18640\n", - " 294.40\n", - " 332.6000\n", - " 216.0000\n", + " ENSG00000169429.10\n", + " 0.5623\n", + " 0.8067\n", + " 116.90000\n", + " 4.047\n", + " 211.0\n", + " 58.110\n", + " 68.38\n", + " 249.50\n", + " 5.095\n", + " 295.9\n", " ...\n", - " 0.2916\n", - " 311.700\n", - " 230.0000\n", - " 302.20000\n", - " 316.500\n", - " 0.2567\n", - " 340.2000\n", - " 0.6962\n", - " 269.1000\n", - " 0.1917\n", + " 39.960\n", + " 0.1393\n", + " 0.22380\n", + " 245.0\n", + " 513.6\n", + " 1626.00\n", + " 0.5633\n", + " 515.70\n", + " 1.19400\n", + " 1163.00\n", " \n", " \n", - " ENSG00000149968.11\n", - " 100.4000\n", - " 785.1000\n", - " 14.0000\n", - " 44.48\n", - " 17.960\n", - " 2.5670\n", - " 0.18410\n", - " 46.91\n", - " 13.9500\n", - " 0.1953\n", + " ENSG00000135245.9\n", + " 0.6529\n", + " 1.3850\n", + " 199.20000\n", + " 2.266\n", + " 116.7\n", + " 192.300\n", + " 161.50\n", + " 263.50\n", + " 23.540\n", + " 251.9\n", " ...\n", - " 3.9480\n", - " 108.800\n", - " 3.8230\n", - " 6.61700\n", - " 11.440\n", - " 7.6190\n", - " 27.4300\n", - " 21.0200\n", - " 122.6000\n", - " 10.8200\n", + " 114.300\n", + " 1.8330\n", + " 0.41150\n", + " 149.0\n", + " 935.3\n", + " 233.60\n", + " 0.8882\n", + " 134.00\n", + " 1.12000\n", + " 295.70\n", " \n", " \n", - " ENSG00000134184.12\n", - " 75.6800\n", - " 0.2281\n", - " 0.2070\n", - " 0.00\n", - " 36.930\n", - " 0.1651\n", - " 0.06058\n", - " 174.00\n", - " 0.1429\n", - " 56.4700\n", + " ENSG00000163631.16\n", + " 1.8480\n", + " 0.2503\n", + " 0.08429\n", + " 1.251\n", + " 1348.0\n", + " 9.971\n", + " 101.30\n", + " 95.09\n", + " 1.264\n", + " 119.3\n", " ...\n", - " 54.9200\n", - " 46.230\n", - " 0.1468\n", - " 0.04705\n", - " 67.240\n", - " 0.4005\n", - " 0.5507\n", - " 56.0600\n", - " 0.4048\n", - " 0.0000\n", + " 2.092\n", + " 2.1100\n", + " 0.03588\n", + " 171.8\n", + " 107.1\n", + " 71.25\n", + " 1.7720\n", + " 309.60\n", + " 0.07361\n", + " 17.75\n", " \n", " \n", - " ENSG00000224114.1\n", - " 1.1500\n", - " 0.8068\n", - " 0.5856\n", - " 74.28\n", - " 0.314\n", - " 0.6115\n", - " 49.95000\n", - " 139.60\n", - " 83.5400\n", - " 1.3640\n", + " ENSG00000277632.1\n", + " 1.6960\n", + " 1.3450\n", + " 235.10000\n", + " 11.770\n", + " 141.7\n", + " 199.100\n", + " 525.50\n", + " 659.90\n", + " 10.910\n", + " 209.3\n", " ...\n", - " 0.1915\n", - " 5.593\n", - " 60.0200\n", - " 61.04000\n", - " 1.596\n", - " 81.6000\n", - " 149.4000\n", - " 0.2032\n", - " 1.2270\n", - " 0.5036\n", + " 61.340\n", + " 2.2500\n", + " 0.72310\n", + " 261.2\n", + " 400.0\n", + " 288.50\n", + " 2.6960\n", + " 287.50\n", + " 3.32300\n", + " 618.90\n", " \n", " \n", - " ENSG00000173432.10\n", - " 2765.0000\n", - " 241.1000\n", - " 1.5220\n", - " 99.98\n", - " 921.400\n", - " 2859.0000\n", - " 3874.00000\n", - " 21.41\n", - " 1338.0000\n", - " 61.4800\n", + " ENSG00000239839.6\n", + " 185.2000\n", + " 1.7790\n", + " 694.30000\n", + " 23.840\n", + " 297.3\n", + " 3122.000\n", + " 2521.00\n", + " 1504.00\n", + " 80.060\n", + " 652.0\n", " ...\n", - " 1666.0000\n", - " 165.300\n", - " 81.9700\n", - " 180.90000\n", - " 24.650\n", - " 276.2000\n", - " 53.5400\n", - " 1436.0000\n", - " 140.5000\n", - " 756.3000\n", + " 1010.000\n", + " 253.8000\n", + " 94.52000\n", + " 6083.0\n", + " 2768.0\n", + " 52.06\n", + " 34.5700\n", + " 17.36\n", + " 352.30000\n", + " 63.85\n", " \n", " \n", "\n", - "

5 rows × 663 columns

\n", + "

5 rows × 755 columns

\n", "" ], "text/plain": [ - " GTEX-1117F-0226-SM-5GZZ7 GTEX-111CU-1826-SM-5GZYN \\\n", + " GTEX-111YS-0006-SM-5NQBE GTEX-1122O-0005-SM-5O99J \\\n", "gene_ens_id \n", - "ENSG00000129824.15 0.9301 270.4000 \n", - "ENSG00000149968.11 100.4000 785.1000 \n", - "ENSG00000134184.12 75.6800 0.2281 \n", - "ENSG00000224114.1 1.1500 0.8068 \n", - "ENSG00000173432.10 2765.0000 241.1000 \n", + "ENSG00000169429.10 0.5623 0.8067 \n", + "ENSG00000135245.9 0.6529 1.3850 \n", + "ENSG00000163631.16 1.8480 0.2503 \n", + "ENSG00000277632.1 1.6960 1.3450 \n", + "ENSG00000239839.6 185.2000 1.7790 \n", "\n", - " GTEX-111FC-0226-SM-5N9B8 GTEX-111VG-2326-SM-5N9BK \\\n", + " GTEX-1128S-0005-SM-5P9HI GTEX-113IC-0006-SM-5NQ9C \\\n", "gene_ens_id \n", - "ENSG00000129824.15 345.8000 242.20 \n", - "ENSG00000149968.11 14.0000 44.48 \n", - "ENSG00000134184.12 0.2070 0.00 \n", - "ENSG00000224114.1 0.5856 74.28 \n", - "ENSG00000173432.10 1.5220 99.98 \n", + "ENSG00000169429.10 116.90000 4.047 \n", + "ENSG00000135245.9 199.20000 2.266 \n", + "ENSG00000163631.16 0.08429 1.251 \n", + "ENSG00000277632.1 235.10000 11.770 \n", + "ENSG00000239839.6 694.30000 23.840 \n", "\n", - " GTEX-111YS-2426-SM-5GZZQ GTEX-1122O-2026-SM-9YFMG \\\n", + " GTEX-113JC-0006-SM-5O997 GTEX-117XS-0005-SM-5PNU6 \\\n", "gene_ens_id \n", - "ENSG00000129824.15 180.800 0.1904 \n", - "ENSG00000149968.11 17.960 2.5670 \n", - "ENSG00000134184.12 36.930 0.1651 \n", - "ENSG00000224114.1 0.314 0.6115 \n", - "ENSG00000173432.10 921.400 2859.0000 \n", + "ENSG00000169429.10 211.0 58.110 \n", + "ENSG00000135245.9 116.7 192.300 \n", + "ENSG00000163631.16 1348.0 9.971 \n", + "ENSG00000277632.1 141.7 199.100 \n", + "ENSG00000239839.6 297.3 3122.000 \n", "\n", - " GTEX-1128S-2126-SM-5H12U GTEX-113IC-0226-SM-5HL5C \\\n", + " GTEX-117YW-0005-SM-5NQ8Z GTEX-1192W-0005-SM-5NQBQ \\\n", "gene_ens_id \n", - "ENSG00000129824.15 0.18640 294.40 \n", - "ENSG00000149968.11 0.18410 46.91 \n", - "ENSG00000134184.12 0.06058 174.00 \n", - "ENSG00000224114.1 49.95000 139.60 \n", - "ENSG00000173432.10 3874.00000 21.41 \n", + "ENSG00000169429.10 68.38 249.50 \n", + "ENSG00000135245.9 161.50 263.50 \n", + "ENSG00000163631.16 101.30 95.09 \n", + "ENSG00000277632.1 525.50 659.90 \n", + "ENSG00000239839.6 2521.00 1504.00 \n", "\n", - " GTEX-117YX-2226-SM-5EGJJ GTEX-11DXW-0326-SM-5H11W ... \\\n", + " GTEX-1192X-0005-SM-5NQC3 GTEX-11DXW-0006-SM-5NQ7Y ... \\\n", "gene_ens_id ... \n", - "ENSG00000129824.15 332.6000 216.0000 ... \n", - "ENSG00000149968.11 13.9500 0.1953 ... \n", - "ENSG00000134184.12 0.1429 56.4700 ... \n", - "ENSG00000224114.1 83.5400 1.3640 ... \n", - "ENSG00000173432.10 1338.0000 61.4800 ... \n", + "ENSG00000169429.10 5.095 295.9 ... \n", + "ENSG00000135245.9 23.540 251.9 ... \n", + "ENSG00000163631.16 1.264 119.3 ... \n", + "ENSG00000277632.1 10.910 209.3 ... \n", + "ENSG00000239839.6 80.060 652.0 ... \n", "\n", - " GTEX-ZXES-2026-SM-5NQ6R GTEX-ZXG5-0226-SM-59HJI \\\n", + " GTEX-ZVE2-0006-SM-51MRW GTEX-ZVP2-0005-SM-51MRK \\\n", "gene_ens_id \n", - "ENSG00000129824.15 0.2916 311.700 \n", - "ENSG00000149968.11 3.9480 108.800 \n", - "ENSG00000134184.12 54.9200 46.230 \n", - "ENSG00000224114.1 0.1915 5.593 \n", - "ENSG00000173432.10 1666.0000 165.300 \n", + "ENSG00000169429.10 39.960 0.1393 \n", + "ENSG00000135245.9 114.300 1.8330 \n", + "ENSG00000163631.16 2.092 2.1100 \n", + "ENSG00000277632.1 61.340 2.2500 \n", + "ENSG00000239839.6 1010.000 253.8000 \n", "\n", - " GTEX-ZYFC-0326-SM-5NQ7H GTEX-ZYFD-0226-SM-5NQ86 \\\n", + " GTEX-ZVT2-0005-SM-57WBW GTEX-ZVT3-0006-SM-51MT9 \\\n", "gene_ens_id \n", - "ENSG00000129824.15 230.0000 302.20000 \n", - "ENSG00000149968.11 3.8230 6.61700 \n", - "ENSG00000134184.12 0.1468 0.04705 \n", - "ENSG00000224114.1 60.0200 61.04000 \n", - "ENSG00000173432.10 81.9700 180.90000 \n", + "ENSG00000169429.10 0.22380 245.0 \n", + "ENSG00000135245.9 0.41150 149.0 \n", + "ENSG00000163631.16 0.03588 171.8 \n", + "ENSG00000277632.1 0.72310 261.2 \n", + "ENSG00000239839.6 94.52000 6083.0 \n", "\n", - " GTEX-ZYT6-0326-SM-7LG5R GTEX-ZYVF-0226-SM-5GIEG \\\n", + " GTEX-ZVT4-0006-SM-57WB8 GTEX-ZVTK-0006-SM-57WBK \\\n", "gene_ens_id \n", - "ENSG00000129824.15 316.500 0.2567 \n", - "ENSG00000149968.11 11.440 7.6190 \n", - "ENSG00000134184.12 67.240 0.4005 \n", - "ENSG00000224114.1 1.596 81.6000 \n", - "ENSG00000173432.10 24.650 276.2000 \n", + "ENSG00000169429.10 513.6 1626.00 \n", + "ENSG00000135245.9 935.3 233.60 \n", + "ENSG00000163631.16 107.1 71.25 \n", + "ENSG00000277632.1 400.0 288.50 \n", + "ENSG00000239839.6 2768.0 52.06 \n", "\n", - " GTEX-ZYW4-0226-SM-5E44M GTEX-ZYY3-0226-SM-5E45M \\\n", + " GTEX-ZVZP-0006-SM-51MSW GTEX-ZVZQ-0006-SM-51MR8 \\\n", "gene_ens_id \n", - "ENSG00000129824.15 340.2000 0.6962 \n", - "ENSG00000149968.11 27.4300 21.0200 \n", - "ENSG00000134184.12 0.5507 56.0600 \n", - "ENSG00000224114.1 149.4000 0.2032 \n", - "ENSG00000173432.10 53.5400 1436.0000 \n", + "ENSG00000169429.10 0.5633 515.70 \n", + "ENSG00000135245.9 0.8882 134.00 \n", + "ENSG00000163631.16 1.7720 309.60 \n", + "ENSG00000277632.1 2.6960 287.50 \n", + "ENSG00000239839.6 34.5700 17.36 \n", "\n", - " GTEX-ZZ64-1626-SM-5E43W GTEX-ZZPU-2726-SM-5NQ8O \n", + " GTEX-ZXES-0005-SM-57WCB GTEX-ZXG5-0005-SM-57WCN \n", "gene_ens_id \n", - "ENSG00000129824.15 269.1000 0.1917 \n", - "ENSG00000149968.11 122.6000 10.8200 \n", - "ENSG00000134184.12 0.4048 0.0000 \n", - "ENSG00000224114.1 1.2270 0.5036 \n", - "ENSG00000173432.10 140.5000 756.3000 \n", + "ENSG00000169429.10 1.19400 1163.00 \n", + "ENSG00000135245.9 1.12000 295.70 \n", + "ENSG00000163631.16 0.07361 17.75 \n", + "ENSG00000277632.1 3.32300 618.90 \n", + "ENSG00000239839.6 352.30000 63.85 \n", "\n", - "[5 rows x 663 columns]" + "[5 rows x 755 columns]" ] }, - "execution_count": 10, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } @@ -818,10 +827,10 @@ "id": "5903f3f5-791e-4f03-9d79-600102933d04", "metadata": { "papermill": { - "duration": 0.016529, - "end_time": "2022-01-21T05:24:21.055833", + "duration": 0.002391, + "end_time": "2023-09-07T01:00:39.955456", "exception": false, - "start_time": "2022-01-21T05:24:21.039304", + "start_time": "2023-09-07T01:00:39.953065", "status": "completed" }, "tags": [] @@ -832,20 +841,20 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 13, "id": "118a6631-1cfd-44a3-bd85-5ec7118edd03", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:21.092981Z", - "iopub.status.busy": "2022-01-21T05:24:21.092471Z", - "iopub.status.idle": "2022-01-21T05:24:21.099815Z", - "shell.execute_reply": "2022-01-21T05:24:21.099429Z" + "iopub.execute_input": "2023-09-07T01:00:39.961934Z", + "iopub.status.busy": "2023-09-07T01:00:39.961759Z", + "iopub.status.idle": "2023-09-07T01:00:39.965952Z", + "shell.execute_reply": "2023-09-07T01:00:39.965776Z" }, "papermill": { - "duration": 0.027831, - "end_time": "2022-01-21T05:24:21.099943", + "duration": 0.008039, + "end_time": "2023-09-07T01:00:39.966715", "exception": false, - "start_time": "2022-01-21T05:24:21.072112", + "start_time": "2023-09-07T01:00:39.958676", "status": "completed" }, "tags": [] @@ -881,9 +890,9 @@ " \n", " \n", " gene_ens_id\n", - " ENSG00000129824.15\n", - " ENSG00000149968.11\n", - " ENSG00000134184.12\n", + " ENSG00000169429.10\n", + " ENSG00000135245.9\n", + " ENSG00000163631.16\n", " \n", " \n", " gene_ens_id\n", @@ -894,21 +903,21 @@ " \n", " \n", " \n", - " ENSG00000129824.15\n", + " ENSG00000169429.10\n", " 1.000000\n", - " 0.142708\n", - " 0.044838\n", + " 0.571672\n", + " 0.126906\n", " \n", " \n", - " ENSG00000149968.11\n", - " 0.142708\n", + " ENSG00000135245.9\n", + " 0.571672\n", " 1.000000\n", - " -0.007867\n", + " 0.110612\n", " \n", " \n", - " ENSG00000134184.12\n", - " 0.044838\n", - " -0.007867\n", + " ENSG00000163631.16\n", + " 0.126906\n", + " 0.110612\n", " 1.000000\n", " \n", " \n", @@ -916,11 +925,11 @@ "" ], "text/plain": [ - "gene_ens_id ENSG00000129824.15 ENSG00000149968.11 ENSG00000134184.12\n", - "gene_ens_id \n", - "ENSG00000129824.15 1.000000 0.142708 0.044838\n", - "ENSG00000149968.11 0.142708 1.000000 -0.007867\n", - "ENSG00000134184.12 0.044838 -0.007867 1.000000" + "gene_ens_id ENSG00000169429.10 ENSG00000135245.9 ENSG00000163631.16\n", + "gene_ens_id \n", + "ENSG00000169429.10 1.000000 0.571672 0.126906\n", + "ENSG00000135245.9 0.571672 1.000000 0.110612\n", + "ENSG00000163631.16 0.126906 0.110612 1.000000" ] }, "metadata": {}, @@ -936,20 +945,20 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 14, "id": "d32281d8-f640-4f87-a1d5-aefa0757e9c3", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:24:21.139463Z", - "iopub.status.busy": "2022-01-21T05:24:21.139009Z", - "iopub.status.idle": "2022-01-21T05:24:25.078285Z", - "shell.execute_reply": "2022-01-21T05:24:25.078692Z" + "iopub.execute_input": "2023-09-07T01:00:39.971181Z", + "iopub.status.busy": "2023-09-07T01:00:39.971078Z", + "iopub.status.idle": "2023-09-07T01:00:43.582088Z", + "shell.execute_reply": "2023-09-07T01:00:43.581900Z" }, "papermill": { - "duration": 3.960722, - "end_time": "2022-01-21T05:24:25.078804", + "duration": 3.613767, + "end_time": "2023-09-07T01:00:43.582758", "exception": false, - "start_time": "2022-01-21T05:24:21.118082", + "start_time": "2023-09-07T01:00:39.968991", "status": "completed" }, "tags": [] @@ -959,7 +968,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "48.6 ms ± 50.1 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n" + "17.1 ms ± 0 ns per loop (mean ± std. dev. of 1 run, 100 loops each)\n" ] } ], @@ -972,10 +981,10 @@ "id": "fc2f7184-c0da-438c-94f5-002912793636", "metadata": { "papermill": { - "duration": 0.017101, - "end_time": "2022-01-21T05:24:25.128197", + "duration": 0.001782, + "end_time": "2023-09-07T01:00:43.586424", "exception": false, - "start_time": "2022-01-21T05:24:25.111096", + "start_time": "2023-09-07T01:00:43.584642", "status": "completed" }, "tags": [] @@ -986,20 +995,20 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 15, "id": "1237ae45-d4fc-4074-bfc7-a1de75aeea48", "metadata": { "execution": { - 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" GTEX-1117F-0226-SM-5GZZ7\n", - " GTEX-111CU-1826-SM-5GZYN\n", - " GTEX-111FC-0226-SM-5N9B8\n", - " GTEX-111VG-2326-SM-5N9BK\n", - " GTEX-111YS-2426-SM-5GZZQ\n", - " GTEX-1122O-2026-SM-9YFMG\n", - " GTEX-1128S-2126-SM-5H12U\n", - " GTEX-113IC-0226-SM-5HL5C\n", - " GTEX-117YX-2226-SM-5EGJJ\n", - " GTEX-11DXW-0326-SM-5H11W\n", + " GTEX-111YS-0006-SM-5NQBE\n", + " GTEX-1122O-0005-SM-5O99J\n", + " GTEX-1128S-0005-SM-5P9HI\n", + " GTEX-113IC-0006-SM-5NQ9C\n", + " GTEX-113JC-0006-SM-5O997\n", + " GTEX-117XS-0005-SM-5PNU6\n", + " GTEX-117YW-0005-SM-5NQ8Z\n", + " GTEX-1192W-0005-SM-5NQBQ\n", + " GTEX-1192X-0005-SM-5NQC3\n", + " GTEX-11DXW-0006-SM-5NQ7Y\n", " ...\n", - " GTEX-ZXES-2026-SM-5NQ6R\n", - " GTEX-ZXG5-0226-SM-59HJI\n", - " GTEX-ZYFC-0326-SM-5NQ7H\n", - " GTEX-ZYFD-0226-SM-5NQ86\n", - " GTEX-ZYT6-0326-SM-7LG5R\n", - " GTEX-ZYVF-0226-SM-5GIEG\n", - " GTEX-ZYW4-0226-SM-5E44M\n", - " GTEX-ZYY3-0226-SM-5E45M\n", - " GTEX-ZZ64-1626-SM-5E43W\n", - " GTEX-ZZPU-2726-SM-5NQ8O\n", + " GTEX-ZVE2-0006-SM-51MRW\n", + " GTEX-ZVP2-0005-SM-51MRK\n", + " GTEX-ZVT2-0005-SM-57WBW\n", + " GTEX-ZVT3-0006-SM-51MT9\n", + " GTEX-ZVT4-0006-SM-57WB8\n", + " GTEX-ZVTK-0006-SM-57WBK\n", + " GTEX-ZVZP-0006-SM-51MSW\n", + " GTEX-ZVZQ-0006-SM-51MR8\n", + " GTEX-ZXES-0005-SM-57WCB\n", + " GTEX-ZXG5-0005-SM-57WCN\n", " \n", " \n", " gene_ens_id\n", @@ -583,215 +605,215 @@ " \n", " \n", " \n", - 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" 1.1500\n", - " 0.8068\n", - " 0.5856\n", - " 74.28\n", - " 0.314\n", - " 0.6115\n", - " 49.95000\n", - " 139.60\n", - " 83.5400\n", - " 1.3640\n", + " ENSG00000277632.1\n", + " 1.6960\n", + " 1.3450\n", + " 235.10000\n", + " 11.770\n", + " 141.7\n", + " 199.100\n", + " 525.50\n", + " 659.90\n", + " 10.910\n", + " 209.3\n", " ...\n", - " 0.1915\n", - " 5.593\n", - " 60.0200\n", - " 61.04000\n", - " 1.596\n", - " 81.6000\n", - " 149.4000\n", - " 0.2032\n", - " 1.2270\n", - " 0.5036\n", + " 61.340\n", + " 2.2500\n", + " 0.72310\n", + " 261.2\n", + " 400.0\n", + " 288.50\n", + " 2.6960\n", + " 287.50\n", + " 3.32300\n", + " 618.90\n", " \n", " \n", - " ENSG00000173432.10\n", - " 2765.0000\n", - " 241.1000\n", - " 1.5220\n", - " 99.98\n", - " 921.400\n", - " 2859.0000\n", - " 3874.00000\n", - " 21.41\n", - " 1338.0000\n", - " 61.4800\n", + " ENSG00000239839.6\n", + " 185.2000\n", + " 1.7790\n", + " 694.30000\n", + " 23.840\n", + " 297.3\n", + " 3122.000\n", + " 2521.00\n", + " 1504.00\n", + " 80.060\n", + " 652.0\n", " ...\n", - 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5 rows × 663 columns

\n", + "

5 rows × 755 columns

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" GTEX-ZYW4-0226-SM-5E44M GTEX-ZYY3-0226-SM-5E45M \\\n", + " GTEX-ZVZP-0006-SM-51MSW GTEX-ZVZQ-0006-SM-51MR8 \\\n", "gene_ens_id \n", - "ENSG00000129824.15 340.2000 0.6962 \n", - "ENSG00000149968.11 27.4300 21.0200 \n", - "ENSG00000134184.12 0.5507 56.0600 \n", - "ENSG00000224114.1 149.4000 0.2032 \n", - "ENSG00000173432.10 53.5400 1436.0000 \n", + "ENSG00000169429.10 0.5633 515.70 \n", + "ENSG00000135245.9 0.8882 134.00 \n", + "ENSG00000163631.16 1.7720 309.60 \n", + "ENSG00000277632.1 2.6960 287.50 \n", + "ENSG00000239839.6 34.5700 17.36 \n", "\n", - " GTEX-ZZ64-1626-SM-5E43W GTEX-ZZPU-2726-SM-5NQ8O \n", + " GTEX-ZXES-0005-SM-57WCB GTEX-ZXG5-0005-SM-57WCN \n", "gene_ens_id \n", - "ENSG00000129824.15 269.1000 0.1917 \n", - "ENSG00000149968.11 122.6000 10.8200 \n", - "ENSG00000134184.12 0.4048 0.0000 \n", - "ENSG00000224114.1 1.2270 0.5036 \n", - "ENSG00000173432.10 140.5000 756.3000 \n", + "ENSG00000169429.10 1.19400 1163.00 \n", + "ENSG00000135245.9 1.12000 295.70 \n", + "ENSG00000163631.16 0.07361 17.75 \n", + "ENSG00000277632.1 3.32300 618.90 \n", + "ENSG00000239839.6 352.30000 63.85 \n", "\n", - "[5 rows x 663 columns]" + "[5 rows x 755 columns]" ] }, - "execution_count": 10, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } @@ -805,10 +827,10 @@ "id": "5903f3f5-791e-4f03-9d79-600102933d04", "metadata": { "papermill": { - "duration": 0.016489, - "end_time": "2022-01-21T05:27:05.146066", + "duration": 0.001461, + "end_time": "2023-09-07T01:00:47.490124", "exception": false, - "start_time": "2022-01-21T05:27:05.129577", + "start_time": "2023-09-07T01:00:47.488663", "status": "completed" }, "tags": [] @@ -819,20 +841,20 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 13, "id": "118a6631-1cfd-44a3-bd85-5ec7118edd03", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:27:05.181291Z", - "iopub.status.busy": "2022-01-21T05:27:05.180823Z", - "iopub.status.idle": "2022-01-21T05:27:05.189078Z", - "shell.execute_reply": "2022-01-21T05:27:05.188704Z" + "iopub.execute_input": "2023-09-07T01:00:47.493589Z", + "iopub.status.busy": "2023-09-07T01:00:47.493466Z", + "iopub.status.idle": "2023-09-07T01:00:47.496815Z", + "shell.execute_reply": "2023-09-07T01:00:47.496692Z" }, "papermill": { - "duration": 0.027234, - "end_time": "2022-01-21T05:27:05.189174", + "duration": 0.005534, + "end_time": "2023-09-07T01:00:47.497193", "exception": false, - "start_time": "2022-01-21T05:27:05.161940", + "start_time": "2023-09-07T01:00:47.491659", "status": "completed" }, "tags": [] @@ -868,9 +890,9 @@ " \n", " \n", " gene_ens_id\n", - " ENSG00000129824.15\n", - " ENSG00000149968.11\n", - " ENSG00000134184.12\n", + " ENSG00000169429.10\n", + " ENSG00000135245.9\n", + " ENSG00000163631.16\n", " \n", " \n", " gene_ens_id\n", @@ -881,21 +903,21 @@ " \n", " \n", " \n", - " ENSG00000129824.15\n", + " ENSG00000169429.10\n", " 1.000000\n", - " 0.404501\n", - " 0.016874\n", + " 0.853836\n", + " 0.709240\n", " \n", " \n", - " ENSG00000149968.11\n", - " 0.404501\n", + " ENSG00000135245.9\n", + " 0.853836\n", " 1.000000\n", - " -0.062548\n", + " 0.675719\n", " \n", " \n", - " ENSG00000134184.12\n", - " 0.016874\n", - " -0.062548\n", + " ENSG00000163631.16\n", + " 0.709240\n", + " 0.675719\n", " 1.000000\n", " \n", " \n", @@ -903,11 +925,11 @@ "" ], "text/plain": [ - "gene_ens_id ENSG00000129824.15 ENSG00000149968.11 ENSG00000134184.12\n", - "gene_ens_id \n", - "ENSG00000129824.15 1.000000 0.404501 0.016874\n", - "ENSG00000149968.11 0.404501 1.000000 -0.062548\n", - "ENSG00000134184.12 0.016874 -0.062548 1.000000" + "gene_ens_id ENSG00000169429.10 ENSG00000135245.9 ENSG00000163631.16\n", + "gene_ens_id \n", + "ENSG00000169429.10 1.000000 0.853836 0.709240\n", + "ENSG00000135245.9 0.853836 1.000000 0.675719\n", + "ENSG00000163631.16 0.709240 0.675719 1.000000" ] }, "metadata": {}, @@ -923,20 +945,20 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 14, "id": "d32281d8-f640-4f87-a1d5-aefa0757e9c3", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:27:05.227237Z", - "iopub.status.busy": "2022-01-21T05:27:05.226787Z", - "iopub.status.idle": "2022-01-21T05:27:10.765426Z", - "shell.execute_reply": "2022-01-21T05:27:10.764976Z" + "iopub.execute_input": "2023-09-07T01:00:47.500602Z", + "iopub.status.busy": "2023-09-07T01:00:47.500519Z", + "iopub.status.idle": "2023-09-07T01:00:48.124696Z", + "shell.execute_reply": "2023-09-07T01:00:48.124427Z" }, "papermill": { - "duration": 5.558914, - "end_time": "2022-01-21T05:27:10.765525", + "duration": 0.62651, + "end_time": "2023-09-07T01:00:48.125294", "exception": false, - "start_time": "2022-01-21T05:27:05.206611", + "start_time": "2023-09-07T01:00:47.498784", "status": "completed" }, "tags": [] @@ -946,7 +968,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "68.4 ms ± 318 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n" + "29.6 ms ± 0 ns per loop (mean ± std. dev. of 1 run, 10 loops each)\n" ] } ], @@ -959,10 +981,10 @@ "id": "fc2f7184-c0da-438c-94f5-002912793636", "metadata": { "papermill": { - "duration": 0.017033, - "end_time": "2022-01-21T05:27:10.800155", + "duration": 0.001677, + "end_time": "2023-09-07T01:00:48.128762", "exception": false, - "start_time": "2022-01-21T05:27:10.783122", + "start_time": "2023-09-07T01:00:48.127085", "status": "completed" }, "tags": [] @@ -973,20 +995,20 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 15, "id": "1237ae45-d4fc-4074-bfc7-a1de75aeea48", "metadata": { "execution": { - "iopub.execute_input": "2022-01-21T05:27:10.839329Z", - "iopub.status.busy": "2022-01-21T05:27:10.838809Z", - "iopub.status.idle": "2022-01-21T05:29:52.217400Z", - "shell.execute_reply": "2022-01-21T05:29:52.216435Z" + "iopub.execute_input": "2023-09-07T01:00:48.132464Z", + "iopub.status.busy": "2023-09-07T01:00:48.132407Z", + "iopub.status.idle": "2023-09-07T01:00:50.298257Z", + "shell.execute_reply": "2023-09-07T01:00:50.298068Z" }, "papermill": { - "duration": 161.400268, - "end_time": "2022-01-21T05:29:52.217491", + "duration": 2.168336, + "end_time": "2023-09-07T01:00:50.298864", "exception": false, - "start_time": "2022-01-21T05:27:10.817223", + "start_time": "2023-09-07T01:00:48.130528", "status": "completed" }, "tags": [] @@ -996,7 +1018,23 @@ "name": "stderr", "output_type": "stream", "text": [ - "gtex_v8_data_whole_blood-var_pc_log2: 100%|█████████████████████████| 54/54 [02:41<00:00, 2.99s/it]\n" + "gtex_v8_data_whole_blood-var_pc_log2: 0%| | 0/1 [00:00\n", " \n", " \n", - " clustermatch\n", + " ccc\n", " pearson\n", " spearman\n", " \n", @@ -2619,15 +2619,15 @@ "" ], "text/plain": [ - " clustermatch pearson spearman\n", - "ENSG00000000419.12 ENSG00000002834.17 0.418721 0.681847 0.786595\n", - " ENSG00000002919.14 0.405090 0.734699 0.816991\n", - " ENSG00000002933.7 0.007466 0.013825 0.004128\n", - " ENSG00000003402.19 0.391683 0.727347 0.803653\n", - " ENSG00000004478.7 0.099013 0.094147 0.231269" + " ccc pearson spearman\n", + "ENSG00000000419.12 ENSG00000002834.17 0.418721 0.681847 0.786595\n", + " ENSG00000002919.14 0.405090 0.734699 0.816991\n", + " ENSG00000002933.7 0.007466 0.013825 0.004128\n", + " ENSG00000003402.19 0.391683 0.727347 0.803653\n", + " ENSG00000004478.7 0.099013 0.094147 0.231269" ] }, - "execution_count": 44, + "execution_count": 43, "metadata": {}, "output_type": "execute_result" } @@ -2641,10 +2641,10 @@ "id": "24a50051-141d-4ba0-ad33-3123b4afc1b6", "metadata": { "papermill": { - "duration": 0.03998, - "end_time": "2022-01-24T16:39:09.723193", + "duration": 0.003329, + "end_time": "2023-09-07T18:55:34.757826", "exception": false, - "start_time": "2022-01-24T16:39:09.683213", + "start_time": "2023-09-07T18:55:34.754497", "status": "completed" }, "tags": [] @@ -2655,20 +2655,20 @@ }, { "cell_type": "code", - "execution_count": 45, + "execution_count": 44, "id": "2f20fdf4-a44a-48c0-bbe1-8def473ac2a5", "metadata": { "execution": { - "iopub.execute_input": "2022-01-24T16:39:09.807006Z", - "iopub.status.busy": "2022-01-24T16:39:09.806543Z", - "iopub.status.idle": "2022-01-24T16:39:09.993322Z", - "shell.execute_reply": "2022-01-24T16:39:09.992766Z" + "iopub.execute_input": "2023-09-07T18:55:34.764918Z", + "iopub.status.busy": "2023-09-07T18:55:34.764853Z", + "iopub.status.idle": "2023-09-07T18:55:34.936622Z", + "shell.execute_reply": "2023-09-07T18:55:34.936430Z" }, "papermill": { - "duration": 0.229981, - "end_time": "2022-01-24T16:39:09.993435", + "duration": 0.176352, + "end_time": "2023-09-07T18:55:34.937535", "exception": false, - "start_time": "2022-01-24T16:39:09.763454", + "start_time": "2023-09-07T18:55:34.761183", "status": "completed" }, "tags": [] @@ -2684,10 +2684,10 @@ "id": "8f464a7f-b76f-4898-8bf5-074eabd33626", "metadata": { "papermill": { - "duration": 0.040435, - "end_time": "2022-01-24T16:39:10.077889", + "duration": 0.003456, + "end_time": "2023-09-07T18:55:34.944719", "exception": false, - "start_time": "2022-01-24T16:39:10.037454", + "start_time": "2023-09-07T18:55:34.941263", "status": "completed" }, "tags": [] @@ -2720,8 +2720,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 53.158221, - "end_time": "2022-01-24T16:39:10.324915", + "duration": 21.618719, + "end_time": "2023-09-07T18:55:35.062437", "environment_variables": {}, "exception": null, "input_path": "nbs/10_compute_correlations/05_gtex_v8/50-combine_all.ipynb", @@ -2729,7 +2729,7 @@ "parameters": { "GTEX_TISSUE": "skin_sun_exposed_lower_leg" }, - "start_time": "2022-01-24T16:38:17.166694", + "start_time": "2023-09-07T18:55:13.443718", "version": "2.3.3" } }, diff --git a/nbs/10_compute_correlations/05_gtex_v8/py/07_01-gtex-var_pc_log2-ccc.py b/nbs/10_compute_correlations/05_gtex_v8/py/07_01-gtex-var_pc_log2-ccc.py index 05381e2e..a255a182 100644 --- a/nbs/10_compute_correlations/05_gtex_v8/py/07_01-gtex-var_pc_log2-ccc.py +++ b/nbs/10_compute_correlations/05_gtex_v8/py/07_01-gtex-var_pc_log2-ccc.py @@ -51,6 +51,9 @@ # "Artery - Tibial", ] +# %% tags=[] +conf.GENERAL["N_JOBS"] + # %% tags=[] CORRELATION_METHOD = lambda x: ccc(x, n_jobs=conf.GENERAL["N_JOBS"]) CORRELATION_METHOD.__name__ = "ccc" diff --git a/nbs/10_compute_correlations/05_gtex_v8/py/08_01-gtex-var_pc_log2-mic_e-parallel.py b/nbs/10_compute_correlations/05_gtex_v8/py/08_01-gtex-var_pc_log2-mic_e-parallel.py index 3ff685ef..fea487c9 100644 --- a/nbs/10_compute_correlations/05_gtex_v8/py/08_01-gtex-var_pc_log2-mic_e-parallel.py +++ b/nbs/10_compute_correlations/05_gtex_v8/py/08_01-gtex-var_pc_log2-mic_e-parallel.py @@ -50,6 +50,9 @@ # "Artery - Tibial", ] +# %% tags=[] +conf.GENERAL["N_JOBS"] + # %% tags=[] def mic_parallel(data):