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
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@@ -200,20 +200,20 @@
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@@ -280,20 +280,20 @@
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@@ -334,20 +334,45 @@
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+ "outputs": [],
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+ "tissue_in_file_names = [f\"_data_{simplify_string(t.lower())}-\" for t in TISSUES]"
+ ]
+ },
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@@ -356,7 +381,7 @@
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@@ -365,29 +390,13 @@
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- " 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')]"
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@@ -457,7 +466,7 @@
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+ "PosixPath('/opt/data/results/gtex_v8/gene_selection/gtex_v8_data_whole_blood-var_pc_log2.pkl')"
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+ "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 @@
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{
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+ "execution_count": 14,
"id": "d32281d8-f640-4f87-a1d5-aefa0757e9c3",
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+ "start_time": "2023-09-07T01:00:39.968991",
"status": "completed"
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"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 @@
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"metadata": {
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"status": "completed"
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"tags": []
@@ -986,20 +995,20 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 15,
"id": "1237ae45-d4fc-4074-bfc7-a1de75aeea48",
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- "end_time": "2022-01-21T05:27:00.176905",
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"exception": false,
- "start_time": "2022-01-21T05:24:25.145752",
+ "start_time": "2023-09-07T01:00:43.588312",
"status": "completed"
},
"tags": []
@@ -1009,7 +1018,23 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "gtex_v8_data_whole_blood-var_pc_log2: 100%|█████████████████████████| 54/54 [02:35<00:00, 2.87s/it]\n"
+ "gtex_v8_data_whole_blood-var_pc_log2: 0%| | 0/1 [00:00, ?it/s]"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "1.7388567924499512"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "gtex_v8_data_whole_blood-var_pc_log2: 100%|███████████████████████████| 1/1 [00:01<00:00, 1.82s/it]\n"
]
}
],
@@ -1042,10 +1067,10 @@
"id": "258babdf-03ce-4450-ab22-7a3d75bf6869",
"metadata": {
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"exception": false,
- "start_time": "2022-01-21T05:27:00.223067",
+ "start_time": "2023-09-07T01:00:45.412305",
"status": "completed"
},
"tags": []
@@ -1078,14 +1103,14 @@
},
"papermill": {
"default_parameters": {},
- "duration": 161.894784,
- "end_time": "2022-01-21T05:27:00.622937",
+ "duration": 6.767244,
+ "end_time": "2023-09-07T01:00:45.534810",
"environment_variables": {},
"exception": null,
"input_path": "nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.ipynb",
"output_path": "nbs/10_compute_correlations/05_gtex_v8/05_01-gtex-var_pc_log2-pearson.run.ipynb",
"parameters": {},
- "start_time": "2022-01-21T05:24:18.728153",
+ "start_time": "2023-09-07T01:00:38.767566",
"version": "2.3.3"
}
},
diff --git a/nbs/10_compute_correlations/05_gtex_v8/06_01-gtex-var_pc_log2-spearman.ipynb b/nbs/10_compute_correlations/05_gtex_v8/06_01-gtex-var_pc_log2-spearman.ipynb
index cf32729a..bd7ffbf0 100644
--- a/nbs/10_compute_correlations/05_gtex_v8/06_01-gtex-var_pc_log2-spearman.ipynb
+++ b/nbs/10_compute_correlations/05_gtex_v8/06_01-gtex-var_pc_log2-spearman.ipynb
@@ -5,10 +5,10 @@
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"metadata": {
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"exception": false,
- "start_time": "2022-01-21T05:27:04.046300",
+ "start_time": "2023-09-07T01:00:47.149484",
"status": "completed"
},
"tags": []
@@ -22,10 +22,10 @@
"id": "57f34c74-404d-4776-b547-e6acb2df75d7",
"metadata": {
"papermill": {
- "duration": 0.012804,
- "end_time": "2022-01-21T05:27:04.122836",
+ "duration": 0.001185,
+ "end_time": "2023-09-07T01:00:47.154346",
"exception": false,
- "start_time": "2022-01-21T05:27:04.110032",
+ "start_time": "2023-09-07T01:00:47.153161",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"id": "1d8fae6b-e623-46a6-aff6-d7849163c820",
"metadata": {
"papermill": {
- "duration": 0.012894,
- "end_time": "2022-01-21T05:27:04.148534",
+ "duration": 0.001262,
+ "end_time": "2023-09-07T01:00:47.158290",
"exception": false,
- "start_time": "2022-01-21T05:27:04.135640",
+ "start_time": "2023-09-07T01:00:47.157028",
"status": "completed"
},
"tags": []
@@ -60,16 +60,16 @@
"id": "76729f0e-f742-495b-b676-d9d7b1539e10",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.180988Z",
- "iopub.status.busy": "2022-01-21T05:27:04.180528Z",
- "iopub.status.idle": "2022-01-21T05:27:04.627027Z",
- "shell.execute_reply": "2022-01-21T05:27:04.626501Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.161465Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.161328Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.379656Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.379392Z"
},
"papermill": {
- "duration": 0.465647,
- "end_time": "2022-01-21T05:27:04.627139",
+ "duration": 0.220992,
+ "end_time": "2023-09-07T01:00:47.380602",
"exception": false,
- "start_time": "2022-01-21T05:27:04.161492",
+ "start_time": "2023-09-07T01:00:47.159610",
"status": "completed"
},
"tags": []
@@ -91,10 +91,10 @@
"id": "a6c3a546-9a49-45e7-9f17-fbdb5af4bfb6",
"metadata": {
"papermill": {
- "duration": 0.012816,
- "end_time": "2022-01-21T05:27:04.653690",
+ "duration": 0.00965,
+ "end_time": "2023-09-07T01:00:47.391842",
"exception": false,
- "start_time": "2022-01-21T05:27:04.640874",
+ "start_time": "2023-09-07T01:00:47.382192",
"status": "completed"
},
"tags": []
@@ -109,16 +109,16 @@
"id": "56ff94d3-a230-4028-a71d-518ac109209b",
"metadata": {
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- "iopub.execute_input": "2022-01-21T05:27:04.683053Z",
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- "shell.execute_reply": "2022-01-21T05:27:04.684580Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.399947Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.399872Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.401946Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.401654Z"
},
"papermill": {
- "duration": 0.018037,
- "end_time": "2022-01-21T05:27:04.684698",
+ "duration": 0.006204,
+ "end_time": "2023-09-07T01:00:47.402741",
"exception": false,
- "start_time": "2022-01-21T05:27:04.666661",
+ "start_time": "2023-09-07T01:00:47.396537",
"status": "completed"
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"tags": []
@@ -130,9 +130,22 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"id": "a9b9f8b2",
"metadata": {
+ "execution": {
+ "iopub.execute_input": "2023-09-07T01:00:47.407682Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.407575Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.409888Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.409600Z"
+ },
+ "papermill": {
+ "duration": 0.006153,
+ "end_time": "2023-09-07T01:00:47.410967",
+ "exception": false,
+ "start_time": "2023-09-07T01:00:47.404814",
+ "status": "completed"
+ },
"tags": []
},
"outputs": [],
@@ -149,20 +162,20 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 4,
"id": "8baf4209-ba56-4e3d-b60f-6ce2bb686159",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.719133Z",
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- "iopub.status.idle": "2022-01-21T05:27:04.722136Z",
- "shell.execute_reply": "2022-01-21T05:27:04.721686Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.416107Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.416016Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.420226Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.420015Z"
},
"papermill": {
- "duration": 0.023934,
- "end_time": "2022-01-21T05:27:04.722233",
+ "duration": 0.007553,
+ "end_time": "2023-09-07T01:00:47.421149",
"exception": false,
- "start_time": "2022-01-21T05:27:04.698299",
+ "start_time": "2023-09-07T01:00:47.413596",
"status": "completed"
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"tags": []
@@ -187,20 +200,20 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 5,
"id": "21a3e349-9a09-4d24-89e3-915fdbf08a81",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.752941Z",
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- "iopub.status.idle": "2022-01-21T05:27:04.753952Z",
- "shell.execute_reply": "2022-01-21T05:27:04.754304Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.425093Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.424974Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.426203Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.426056Z"
},
"papermill": {
- "duration": 0.018105,
- "end_time": "2022-01-21T05:27:04.754415",
+ "duration": 0.003661,
+ "end_time": "2023-09-07T01:00:47.426807",
"exception": false,
- "start_time": "2022-01-21T05:27:04.736310",
+ "start_time": "2023-09-07T01:00:47.423146",
"status": "completed"
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"tags": []
@@ -215,10 +228,10 @@
"id": "b0afcba9-5847-414e-b448-f0cd08ecd8ce",
"metadata": {
"papermill": {
- "duration": 0.013305,
- "end_time": "2022-01-21T05:27:04.781426",
+ "duration": 0.001252,
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"exception": false,
- "start_time": "2022-01-21T05:27:04.768121",
+ "start_time": "2023-09-07T01:00:47.428233",
"status": "completed"
},
"tags": []
@@ -229,20 +242,20 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"id": "35760114-8560-4a0e-ad4f-2bee9104c63d",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.812358Z",
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- "iopub.status.idle": "2022-01-21T05:27:04.814255Z",
- "shell.execute_reply": "2022-01-21T05:27:04.814619Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.432526Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.432441Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.434015Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.433888Z"
},
"papermill": {
- "duration": 0.020015,
- "end_time": "2022-01-21T05:27:04.814733",
+ "duration": 0.003615,
+ "end_time": "2023-09-07T01:00:47.434557",
"exception": false,
- "start_time": "2022-01-21T05:27:04.794718",
+ "start_time": "2023-09-07T01:00:47.430942",
"status": "completed"
},
"tags": []
@@ -267,20 +280,20 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"id": "f1418e81-4e77-4f67-b5ed-b29b797e31a0",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.847292Z",
- "iopub.status.busy": "2022-01-21T05:27:04.846749Z",
- "iopub.status.idle": "2022-01-21T05:27:04.849601Z",
- "shell.execute_reply": "2022-01-21T05:27:04.849166Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.437475Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.437390Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.439008Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.438882Z"
},
"papermill": {
- "duration": 0.020466,
- "end_time": "2022-01-21T05:27:04.849692",
+ "duration": 0.003625,
+ "end_time": "2023-09-07T01:00:47.439506",
"exception": false,
- "start_time": "2022-01-21T05:27:04.829226",
+ "start_time": "2023-09-07T01:00:47.435881",
"status": "completed"
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"tags": []
@@ -307,10 +320,10 @@
"id": "5fdf8df6-eba0-4cf5-979c-3acd56a5ef3c",
"metadata": {
"papermill": {
- "duration": 0.014012,
- "end_time": "2022-01-21T05:27:04.878246",
+ "duration": 0.001248,
+ "end_time": "2023-09-07T01:00:47.442083",
"exception": false,
- "start_time": "2022-01-21T05:27:04.864234",
+ "start_time": "2023-09-07T01:00:47.440835",
"status": "completed"
},
"tags": []
@@ -321,20 +334,45 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"id": "596d25ed-4120-4bef-8984-a91ae6529ab5",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:04.910458Z",
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- "iopub.status.idle": "2022-01-21T05:27:04.914655Z",
- "shell.execute_reply": "2022-01-21T05:27:04.915006Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.444989Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.444892Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.446148Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.446013Z"
+ },
+ "papermill": {
+ "duration": 0.00325,
+ "end_time": "2023-09-07T01:00:47.446665",
+ "exception": false,
+ "start_time": "2023-09-07T01:00:47.443415",
+ "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": "5fadd2c5",
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2023-09-07T01:00:47.449538Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.449456Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.451848Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.451729Z"
},
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- "duration": 0.022631,
- "end_time": "2022-01-21T05:27:04.915117",
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"exception": false,
- "start_time": "2022-01-21T05:27:04.892486",
+ "start_time": "2023-09-07T01:00:47.448002",
"status": "completed"
},
"tags": []
@@ -343,7 +381,7 @@
{
"data": {
"text/plain": [
- "54"
+ "1"
]
},
"metadata": {},
@@ -352,29 +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": "5fadd2c5",
- "metadata": {
- "tags": []
- },
- "outputs": [],
"source": [
"input_files = sorted(list(INPUT_DIR.glob(f\"*-{GENE_SELECTION_STRATEGY}.pkl\")))\n",
"input_files = [\n",
@@ -391,10 +413,10 @@
"id": "081da632-fd12-462a-9ae1-c0ceccf1bb5d",
"metadata": {
"papermill": {
- "duration": 0.014562,
- "end_time": "2022-01-21T05:27:04.944643",
+ "duration": 0.00132,
+ "end_time": "2023-09-07T01:00:47.454936",
"exception": false,
- "start_time": "2022-01-21T05:27:04.930081",
+ "start_time": "2023-09-07T01:00:47.453616",
"status": "completed"
},
"tags": []
@@ -408,10 +430,10 @@
"id": "37137fff-2d3a-43d8-9bd5-d7c3284a97f5",
"metadata": {
"papermill": {
- "duration": 0.014593,
- "end_time": "2022-01-21T05:27:04.973725",
+ "duration": 0.001323,
+ "end_time": "2023-09-07T01:00:47.457617",
"exception": false,
- "start_time": "2022-01-21T05:27:04.959132",
+ "start_time": "2023-09-07T01:00:47.456294",
"status": "completed"
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"tags": []
@@ -422,20 +444,20 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 10,
"id": "5dd40707-759f-4bf9-b8cc-84811b2dfe53",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:05.006650Z",
- "iopub.status.busy": "2022-01-21T05:27:05.006132Z",
- "iopub.status.idle": "2022-01-21T05:27:05.019712Z",
- "shell.execute_reply": "2022-01-21T05:27:05.019254Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.460609Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.460523Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.469932Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.469775Z"
},
"papermill": {
- "duration": 0.03141,
- "end_time": "2022-01-21T05:27:05.019809",
+ "duration": 0.011531,
+ "end_time": "2023-09-07T01:00:47.470523",
"exception": false,
- "start_time": "2022-01-21T05:27:04.988399",
+ "start_time": "2023-09-07T01:00:47.458992",
"status": "completed"
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"tags": []
@@ -444,7 +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": {},
@@ -458,20 +480,20 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 11,
"id": "e8acd036-93f7-46c0-a1ee-8da0c2c24790",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:05.054317Z",
- "iopub.status.busy": "2022-01-21T05:27:05.053785Z",
- "iopub.status.idle": "2022-01-21T05:27:05.056668Z",
- "shell.execute_reply": "2022-01-21T05:27:05.056143Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.473750Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.473635Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.475207Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.475085Z"
},
"papermill": {
- "duration": 0.021639,
- "end_time": "2022-01-21T05:27:05.056759",
+ "duration": 0.003641,
+ "end_time": "2023-09-07T01:00:47.475712",
"exception": false,
- "start_time": "2022-01-21T05:27:05.035120",
+ "start_time": "2023-09-07T01:00:47.472071",
"status": "completed"
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"tags": []
@@ -480,10 +502,10 @@
{
"data": {
"text/plain": [
- "(500, 663)"
+ "(500, 755)"
]
},
- "execution_count": 9,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
@@ -494,20 +516,20 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 12,
"id": "111e360b-dbe4-4b69-9029-7b7669eb5ddc",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-21T05:27:05.102738Z",
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- "iopub.status.idle": "2022-01-21T05:27:05.112766Z",
- "shell.execute_reply": "2022-01-21T05:27:05.112380Z"
+ "iopub.execute_input": "2023-09-07T01:00:47.478884Z",
+ "iopub.status.busy": "2023-09-07T01:00:47.478780Z",
+ "iopub.status.idle": "2023-09-07T01:00:47.486401Z",
+ "shell.execute_reply": "2023-09-07T01:00:47.486275Z"
},
"papermill": {
- "duration": 0.039032,
- "end_time": "2022-01-21T05:27:05.112863",
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"exception": false,
- "start_time": "2022-01-21T05:27:05.073831",
+ "start_time": "2023-09-07T01:00:47.477188",
"status": "completed"
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"tags": []
@@ -534,27 +556,27 @@
" \n",
" \n",
" | \n",
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- " GTEX-117YX-2226-SM-5EGJJ | \n",
- " GTEX-11DXW-0326-SM-5H11W | \n",
+ " GTEX-111YS-0006-SM-5NQBE | \n",
+ " GTEX-1122O-0005-SM-5O99J | \n",
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+ " GTEX-1192X-0005-SM-5NQC3 | \n",
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" ... | \n",
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- " GTEX-ZZ64-1626-SM-5E43W | \n",
- " GTEX-ZZPU-2726-SM-5NQ8O | \n",
+ " GTEX-ZVE2-0006-SM-51MRW | \n",
+ " GTEX-ZVP2-0005-SM-51MRK | \n",
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"
\n",
" \n",
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@@ -583,215 +605,215 @@
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\n",
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\n",
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"
\n",
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"
\n",
" \n",
"\n",
- "5 rows × 663 columns
\n",
+ "5 rows × 755 columns
\n",
""
],
"text/plain": [
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"\n",
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+ "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"
}
@@ -805,10 +827,10 @@
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@@ -819,20 +841,20 @@
},
{
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"status": "completed"
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@@ -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 @@
},
{
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"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 @@
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"metadata": {
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@@ -973,20 +995,20 @@
},
{
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- "execution_count": 13,
+ "execution_count": 15,
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+ "iopub.execute_input": "2023-09-07T01:00:48.132464Z",
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},
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"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, ?it/s]"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "2.0522382259368896"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "gtex_v8_data_whole_blood-var_pc_log2: 100%|███████████████████████████| 1/1 [00:02<00:00, 2.16s/it]\n"
]
}
],
@@ -1029,10 +1067,10 @@
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"metadata": {
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@@ -1061,18 +1099,18 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.9.9"
+ "version": "3.9.12"
},
"papermill": {
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"environment_variables": {},
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"input_path": "nbs/10_compute_correlations/05_gtex_v8/06_01-gtex-var_pc_log2-spearman.ipynb",
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"parameters": {},
- "start_time": "2022-01-21T05:27:02.835916",
+ "start_time": "2023-09-07T01:00:46.346515",
"version": "2.3.3"
}
},
diff --git a/nbs/10_compute_correlations/05_gtex_v8/07_01-gtex-var_pc_log2-ccc.ipynb b/nbs/10_compute_correlations/05_gtex_v8/07_01-gtex-var_pc_log2-ccc.ipynb
index 6e42bcc0..d0b22a34 100644
--- a/nbs/10_compute_correlations/05_gtex_v8/07_01-gtex-var_pc_log2-ccc.ipynb
+++ b/nbs/10_compute_correlations/05_gtex_v8/07_01-gtex-var_pc_log2-ccc.ipynb
@@ -5,10 +5,10 @@
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"exception": false,
- "start_time": "2022-05-24T14:46:58.597971",
+ "start_time": "2023-09-07T02:50:46.915064",
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@@ -22,10 +22,10 @@
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"metadata": {
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+ "start_time": "2023-09-07T02:50:46.931357",
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@@ -42,10 +42,10 @@
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"metadata": {
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"exception": false,
- "start_time": "2022-05-24T14:46:58.646543",
+ "start_time": "2023-09-07T02:50:46.943092",
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@@ -60,16 +60,16 @@
"id": "76729f0e-f742-495b-b676-d9d7b1539e10",
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- "shell.execute_reply": "2022-05-24T14:46:59.170627Z"
+ "iopub.execute_input": "2023-09-07T02:50:46.950464Z",
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},
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@@ -91,10 +91,10 @@
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"metadata": {
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+ "start_time": "2023-09-07T02:50:47.180687",
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@@ -109,16 +109,16 @@
"id": "56ff94d3-a230-4028-a71d-518ac109209b",
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- "shell.execute_reply": "2022-05-24T14:46:59.195465Z"
+ "iopub.execute_input": "2023-09-07T02:50:47.196345Z",
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},
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- "start_time": "2022-05-24T14:46:59.187384",
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@@ -134,16 +134,16 @@
"id": "f5433907-5b88-4c68-b3d4-fb98298dec4a",
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@@ -163,19 +163,55 @@
{
"cell_type": "code",
"execution_count": 4,
+ "id": "8fd0656d-e9cc-410b-baa9-96b57538c4c1",
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+ "start_time": "2023-09-07T02:50:47.204704",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "20"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "conf.GENERAL[\"N_JOBS\"]"
+ ]
+ },
+ {
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"id": "8baf4209-ba56-4e3d-b60f-6ce2bb686159",
"metadata": {
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@@ -184,7 +220,7 @@
{
"data": {
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- "'clustermatch'"
+ "'ccc'"
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},
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@@ -201,20 +237,20 @@
},
{
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diff --git a/nbs/10_compute_correlations/05_gtex_v8/08_01-gtex-var_pc_log2-mic_e-parallel.ipynb b/nbs/10_compute_correlations/05_gtex_v8/08_01-gtex-var_pc_log2-mic_e-parallel.ipynb
index cfa53512..06dbce39 100644
--- a/nbs/10_compute_correlations/05_gtex_v8/08_01-gtex-var_pc_log2-mic_e-parallel.ipynb
+++ b/nbs/10_compute_correlations/05_gtex_v8/08_01-gtex-var_pc_log2-mic_e-parallel.ipynb
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@@ -90,10 +90,10 @@
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@@ -108,16 +108,16 @@
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@@ -133,16 +133,16 @@
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@@ -162,19 +162,55 @@
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@@ -203,20 +239,20 @@
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@@ -231,10 +267,10 @@
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@@ -245,20 +281,20 @@
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@@ -283,20 +319,20 @@
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@@ -323,10 +359,10 @@
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@@ -337,20 +373,20 @@
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@@ -362,20 +398,20 @@
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@@ -416,10 +452,10 @@
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@@ -433,10 +469,10 @@
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@@ -447,20 +483,20 @@
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@@ -483,20 +519,20 @@
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@@ -508,7 +544,7 @@
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@@ -519,20 +555,20 @@
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@@ -816,7 +852,7 @@
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@@ -830,10 +866,10 @@
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@@ -844,20 +880,20 @@
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diff --git a/nbs/10_compute_correlations/05_gtex_v8/50-combine_all.ipynb b/nbs/10_compute_correlations/05_gtex_v8/50-combine_all.ipynb
index 85698b5c..4c3ffe3a 100644
--- a/nbs/10_compute_correlations/05_gtex_v8/50-combine_all.ipynb
+++ b/nbs/10_compute_correlations/05_gtex_v8/50-combine_all.ipynb
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- "start_time": "2022-01-24T16:39:09.390660",
+ "start_time": "2023-09-07T18:55:34.703094",
"status": "completed"
},
"tags": []
@@ -2500,20 +2500,20 @@
},
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 42,
"id": "baf842f9-d6c8-48b7-bffe-8eb05c73d7de",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-24T16:39:09.548697Z",
- "iopub.status.busy": "2022-01-24T16:39:09.548014Z",
- "iopub.status.idle": "2022-01-24T16:39:09.551154Z",
- "shell.execute_reply": "2022-01-24T16:39:09.550708Z"
+ "iopub.execute_input": "2023-09-07T18:55:34.738521Z",
+ "iopub.status.busy": "2023-09-07T18:55:34.738365Z",
+ "iopub.status.idle": "2023-09-07T18:55:34.740106Z",
+ "shell.execute_reply": "2023-09-07T18:55:34.739973Z"
},
"papermill": {
- "duration": 0.046311,
- "end_time": "2022-01-24T16:39:09.551248",
+ "duration": 0.005969,
+ "end_time": "2023-09-07T18:55:34.740548",
"exception": false,
- "start_time": "2022-01-24T16:39:09.504937",
+ "start_time": "2023-09-07T18:55:34.734579",
"status": "completed"
},
"tags": []
@@ -2525,7 +2525,7 @@
"(12497500, 3)"
]
},
- "execution_count": 43,
+ "execution_count": 42,
"metadata": {},
"output_type": "execute_result"
}
@@ -2536,20 +2536,20 @@
},
{
"cell_type": "code",
- "execution_count": 44,
+ "execution_count": 43,
"id": "3bd226fe-0c9d-4b69-8250-e22ccaf3730f",
"metadata": {
"execution": {
- "iopub.execute_input": "2022-01-24T16:39:09.639835Z",
- "iopub.status.busy": "2022-01-24T16:39:09.639206Z",
- "iopub.status.idle": "2022-01-24T16:39:09.642428Z",
- "shell.execute_reply": "2022-01-24T16:39:09.641989Z"
+ "iopub.execute_input": "2023-09-07T18:55:34.747574Z",
+ "iopub.status.busy": "2023-09-07T18:55:34.747460Z",
+ "iopub.status.idle": "2023-09-07T18:55:34.750602Z",
+ "shell.execute_reply": "2023-09-07T18:55:34.750463Z"
},
"papermill": {
- "duration": 0.050826,
- "end_time": "2022-01-24T16:39:09.642520",
+ "duration": 0.007234,
+ "end_time": "2023-09-07T18:55:34.751105",
"exception": false,
- "start_time": "2022-01-24T16:39:09.591694",
+ "start_time": "2023-09-07T18:55:34.743871",
"status": "completed"
},
"tags": []
@@ -2577,7 +2577,7 @@
" \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):