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For set enrichment run.
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| [General] | |
| num_iterations = 2000 | |
| num_clusters = 133 | |
| normalize_ratios = False | |
| num_cores = 6 | |
| checkpoint_interval = 100 | |
| stats_frequency = 50 | |
| result_frequency = 50 | |
| [SetEnrichment] | |
| schedule = 1,7 | |
| scaling_rvec = seq(1e-5, 0.5, length=num_iterations/2) | |
| map_to_ratio_genes = True | |
| set_types = targetscan | |
| [SetEnrichment-targetscan] | |
| set_file = targetScan.json | |
| weight = 1.0 |
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| { | |
| "row-scoring": { | |
| "id": "combiner", | |
| "function": { "module": "cmonkey.scoring", "class": "ScoringFunctionCombiner" }, | |
| "args": { | |
| "functions": [ | |
| { "id": "Rows", | |
| "function": { "module": "cmonkey.microarray", "class": "RowScoringFunction" } | |
| }, | |
| { "id": "Networks", | |
| "function": { "module": "cmonkey.network", "class": "ScoringFunction" } | |
| }, | |
| { "id": "SetEnrichment", | |
| "function": { "module": "cmonkey.set_enrichment", "class": "ScoringFunction" } | |
| } | |
| ] | |
| } | |
| }, | |
| "column-scoring": { "id": "Columns", | |
| "function": { "module": "cmonkey.scoring", | |
| "class": "ColumnScoringFunction"} } | |
| } |
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| ./cmonkey.py --organism hsa --ratios norm_gexp_2000_vsn.tsv --pipeline pipeline.json --config cmonkey_setEnrichment.ini --rsat_organism Homo_sapiens --string data/STRING/string.tsv --synonym_file synonymThesaurus.csv.gz |
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 2 columns, instead of 1 in line 2.
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| 5988,ENSG00000128250;ENST00000354373;5988;RFPL1;uc003afn.3 | |
| 5989,ENSG00000132005;ENST00000254325;5989;RFX1;uc002mxv.3;ENST00000588520;ENST00000589239;ENST000005 | |
| 89937;ENST00000589760;ENST00000588885;ENST00000586913 | |
| 83892,ENSG00000110906;ENST00000228495;83892;KCTD10;uc001toi.1;ENST00000540089;uc001tok.1;ENST0000054 | |
| 5759;uc001toh.1;ENST00000440541;ENST00000537165;ENST00000538161;ENST00000540411;uc009zvi.1;ENST00000 | |
| (etc) |
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| { | |
| "hsa-miR-548d-5p": ["121260", "254251", "55765", "64645"], | |
| "hsa-miR-576-3p": ["10000", "10002", "10004", "100133941", "10019", "10026", "1003", "10039", "10050", "10056", "10061", "10079", "10100", "10135", "10138", "10153", "10156", "10162", "10164", "10170", "10193", "10201", "10203", "10205", "10223", "10225", "10231", "1024", "10242", "10251", "10269", "1028", "10289", "103", "10302", "10316", "10328", "10385", "10395", "10396", "1041", "10418", "10419", "10424", "10463", "10472", "10479", "10491", "10495", "10520", "10537", "1054", "10544", "10558", "10560", "10563", "10564", "10566", "10592", "10595", "10599", "10605", "10606", "10611", "10616", "10618", "10621", "10622", "10632", "10640", "10650", "10672", "10687", "10690", "10699", "10721", "10725", "10730", "10735", "10738", "10739", "10752", "10768", "10772", "10794", "108", "1080", "10810", "10842", "10871", "10875", "10891", "10892", "10905", "10914", "10929", "10951", "10964", "10971", "10972", "10985", "11023", "11030", "11037", "11052", "11057", "11069", "11070", "11078", "11083", "1109", "11094", "11098", "11122", "11127", "11144", "11160", "11171", "11194", "11198", "11201", "11214", "1122", "11261", "11270", "112802", "112936", "113", "113189", "113251", "1133", "113419", "1135", "113622", "114134", "114299", "114327", "114569", "114757", "114781"], | |
| (etc) | |
| } |
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