diff --git a/docs/notebooks/09_diff_splice.ipynb b/docs/notebooks/09_diff_splice.ipynb index 3fd5611..45e0cd1 100644 --- a/docs/notebooks/09_diff_splice.ipynb +++ b/docs/notebooks/09_diff_splice.ipynb @@ -775,15 +775,258 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - " 4%|▍ | 477/10803 [00:00<00:04, 2266.87genes/s]" + "100%|██████████| 10803/10803 [00:05<00:00, 2003.31genes/s]\n" ] + }, + { + "data": { + "text/html": [ + "
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gene_idgene_namestrandeventA_typeeventB_typeeventA_startevemtA_endeventB_starteventB_endpvaluepadjstatlog2ORdcPSI_ABdcPSI_BApriA_priBpriA_altBaltA_priBaltA_altBpriA_priB_trIDpriA_altB_trIDaltA_priB_trIDaltA_altB_trID
52ENSG00000147813.16NAPRT-IRIR1435750931435751901435749001435749854.436456e-825.501206e-8098.8952386.6278290.5255520.6371414724514132[0, 5, 6, 7, 54, 62, 73, 17, 100, 24, 30, 46, ...[25, 48, 129, 68, 128, 33, 133, 101, 135, 141,...[41, 96, 110, 112, 115][21, 42, 1, 12, 31, 71, 44, 51, 63, 78, 92, 13...
107ENSG00000182325.11FBXL6-IRIR1443577861443580311443571211443574381.074426e-746.661440e-731715.83333310.7446940.4729270.46975314234145[1, 21, 34, 7, 32, 36, 38, 72, 45, 81, 51, 85,...[89, 87, 71][4, 40][2, 9, 19, 41, 14, 24, 44, 48, 56, 11, 54, 17,...
55ENSG00000167700.9MFSD3+IRIR1445100151445103591445105071445105974.299909e-321.777296e-30inf38.4595950.5038660.74380218020042[0, 3, 23, 35, 5, 38, 39][2, 21, 19, 20, 29][][11, 26, 14, 36, 18]
45ENSG00000160957.15RECQL4-IRIR1445127711445128461445123241445123911.341822e-314.159649e-3011.5291613.5272160.3310310.3445431231878166[22, 31, 6, 20, 114, 147, 124, 11, 38, 72, 13,...[401, 191, 221, 94, 364, 68, 204, 127, 519, 17...[117, 136, 279, 259, 271, 532, 292, 49, 184, 2...[408, 110, 112, 28, 29, 158, 190, 215, 495, 51...
108ENSG00000182325.11FBXL6-IRIR1443577861443580311443569151443569896.335233e-271.571138e-2551.9185195.6981770.2284020.45167216390386[1, 12, 21, 34, 4, 7, 75, 86, 15, 23, 25, 26, ...[2, 3, 41, 24, 44, 48, 8, 17, 37, 6, 18, 33, 5...[32, 53][9, 19, 14, 56, 11, 13, 54, 42, 63, 64, 5, 16,...
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" + ], + "text/plain": [ + " gene_id gene_name strand eventA_type eventB_type \\\n", + "52 ENSG00000147813.16 NAPRT - IR IR \n", + "107 ENSG00000182325.11 FBXL6 - IR IR \n", + "55 ENSG00000167700.9 MFSD3 + IR IR \n", + "45 ENSG00000160957.15 RECQL4 - IR IR \n", + "108 ENSG00000182325.11 FBXL6 - IR IR \n", + "\n", + " eventA_start evemtA_end eventB_start eventB_end pvalue \\\n", + "52 143575093 143575190 143574900 143574985 4.436456e-82 \n", + "107 144357786 144358031 144357121 144357438 1.074426e-74 \n", + "55 144510015 144510359 144510507 144510597 4.299909e-32 \n", + "45 144512771 144512846 144512324 144512391 1.341822e-31 \n", + "108 144357786 144358031 144356915 144356989 6.335233e-27 \n", + "\n", + " padj stat log2OR dcPSI_AB dcPSI_BA priA_priB \\\n", + "52 5.501206e-80 98.895238 6.627829 0.525552 0.637141 472 \n", + "107 6.661440e-73 1715.833333 10.744694 0.472927 0.469753 142 \n", + "55 1.777296e-30 inf 38.459595 0.503866 0.743802 180 \n", + "45 4.159649e-30 11.529161 3.527216 0.331031 0.344543 1231 \n", + "108 1.571138e-25 51.918519 5.698177 0.228402 0.451672 163 \n", + "\n", + " priA_altB altA_priB altA_altB \\\n", + "52 45 14 132 \n", + "107 3 4 145 \n", + "55 20 0 42 \n", + "45 87 81 66 \n", + "108 90 3 86 \n", + "\n", + " priA_priB_trID \\\n", + "52 [0, 5, 6, 7, 54, 62, 73, 17, 100, 24, 30, 46, ... \n", + "107 [1, 21, 34, 7, 32, 36, 38, 72, 45, 81, 51, 85,... \n", + "55 [0, 3, 23, 35, 5, 38, 39] \n", + "45 [22, 31, 6, 20, 114, 147, 124, 11, 38, 72, 13,... \n", + "108 [1, 12, 21, 34, 4, 7, 75, 86, 15, 23, 25, 26, ... \n", + "\n", + " priA_altB_trID \\\n", + "52 [25, 48, 129, 68, 128, 33, 133, 101, 135, 141,... \n", + "107 [89, 87, 71] \n", + "55 [2, 21, 19, 20, 29] \n", + "45 [401, 191, 221, 94, 364, 68, 204, 127, 519, 17... \n", + "108 [2, 3, 41, 24, 44, 48, 8, 17, 37, 6, 18, 33, 5... \n", + "\n", + " altA_priB_trID \\\n", + "52 [41, 96, 110, 112, 115] \n", + "107 [4, 40] \n", + "55 [] \n", + "45 [117, 136, 279, 259, 271, 532, 292, 49, 184, 2... \n", + "108 [32, 53] \n", + "\n", + " altA_altB_trID \n", + "52 [21, 42, 1, 12, 31, 71, 44, 51, 63, 78, 92, 13... \n", + "107 [2, 9, 19, 41, 14, 24, 44, 48, 56, 11, 54, 17,... \n", + "55 [11, 26, 14, 36, 18] \n", + "45 [408, 110, 112, 28, 29, 158, 190, 215, 495, 51... \n", + "108 [9, 19, 14, 56, 11, 13, 54, 42, 63, 64, 5, 16,... " + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ @@ -802,9 +1045,215 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 10803/10803 [00:00<00:00, 14123.06genes/s]\n" + ] + }, + { + "data": { + "text/html": [ + "
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gene_idgene_namechromstrandstartendpadjpvaluedeltaPItranscript_ids
5982ENSG00000070756.17PABPC1chr8-1006858151007228090.000000e+000.000000e+00-0.289084[2, 1]
5094ENSG00000156482.11RPL30chr8-98024850980464690.000000e+000.000000e+000.515042[3, 2]
4805ENSG00000161016.18RPL8chr8-1447897641447925870.000000e+000.000000e+00-0.477042[2, 6]
4632ENSG00000164924.18YWHAZchr8-1009165221009533880.000000e+000.000000e+000.303116[31, 11]
4172ENSG00000147604.14RPL7chr8-73290241732957891.157393e-1701.885004e-1720.092221[2, 31]
3235ENSG00000104408.11EIF3Echr8-1081627861084434962.092139e-1374.088872e-1390.166874[0, 20]
9988ENSG00000104312.8RIPK2chr8+89757805897910646.088181e-1011.388185e-1020.677697[2, 0]
4239ENSG00000129696.13TTI2chr8-33473385335131859.366700e-1002.440834e-101-0.617118[3, 22]
1369ENSG00000147684.10NDUFB9chr8+1245391001245806484.019587e-891.178381e-900.399575[0, -1]
1525ENSG00000104320.15NBNchr8-89924514900032285.103980e-881.662534e-89-0.409024[2, 1]
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" + ], + "text/plain": [ + " gene_id gene_name chrom strand start end \\\n", + "5982 ENSG00000070756.17 PABPC1 chr8 - 100685815 100722809 \n", + "5094 ENSG00000156482.11 RPL30 chr8 - 98024850 98046469 \n", + "4805 ENSG00000161016.18 RPL8 chr8 - 144789764 144792587 \n", + "4632 ENSG00000164924.18 YWHAZ chr8 - 100916522 100953388 \n", + "4172 ENSG00000147604.14 RPL7 chr8 - 73290241 73295789 \n", + "3235 ENSG00000104408.11 EIF3E chr8 - 108162786 108443496 \n", + "9988 ENSG00000104312.8 RIPK2 chr8 + 89757805 89791064 \n", + "4239 ENSG00000129696.13 TTI2 chr8 - 33473385 33513185 \n", + "1369 ENSG00000147684.10 NDUFB9 chr8 + 124539100 124580648 \n", + "1525 ENSG00000104320.15 NBN chr8 - 89924514 90003228 \n", + "\n", + " padj pvalue deltaPI transcript_ids \n", + "5982 0.000000e+00 0.000000e+00 -0.289084 [2, 1] \n", + "5094 0.000000e+00 0.000000e+00 0.515042 [3, 2] \n", + "4805 0.000000e+00 0.000000e+00 -0.477042 [2, 6] \n", + "4632 0.000000e+00 0.000000e+00 0.303116 [31, 11] \n", + "4172 1.157393e-170 1.885004e-172 0.092221 [2, 31] \n", + "3235 2.092139e-137 4.088872e-139 0.166874 [0, 20] \n", + "9988 6.088181e-101 1.388185e-102 0.677697 [2, 0] \n", + "4239 9.366700e-100 2.440834e-101 -0.617118 [3, 22] \n", + "1369 4.019587e-89 1.178381e-90 0.399575 [0, -1] \n", + "1525 5.103980e-88 1.662534e-89 -0.409024 [2, 1] " + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "isoseq.die_test(groups=isoseq.groups()).sort_values('pvalue').head(10)" ]