Hi, I am using Gostats to perform GO enrichment from custom list of genes and custom annotations. My annotation file looks like this head (geneGO) GOterm evi GeneID 1 GO:0016020 ND PCHAS_010020 2 GO:0016021 ND PCHAS_010020 3 GO:0016020 ND PCHAS_010030 4 GO:0016021 ND PCHAS_010030 5 GO:0016020 ND PCHAS_010040 6 GO:0016021 ND PCHAS_010040
My hyperGtest result looks like this >Over.bp.Phase_0_2 <-hyperGTest(params.bp.Phase_0_2 ) >Over.bp.Phase_0_2 Gene to GO BP Conditional test for over-representation 228 GO BP ids tested (45 have p < 0.05) Selected gene set size: 37 Gene universe size: 1707 Annotation package: Based on a GeneSetCollection Object and my summary result looks like this enrichgobp.Phase_9_12 <-summary(Over.bp.Phase_9_12 ) GOBPID Pvalue OddsRatio ExpCount Count Size Term V8 1 GO:0019362 4.441045e-05 17.239583 0.43350908 5 20 pyridine nucleotide metabolic process Phase_0_2 2 GO:0046031 1.163932e-04 22.370370 0.28178090 4 13 ADP metabolic process Phase_0_2 3 GO:0006096 1.163932e-04 22.370370 0.28178090 4 13 glycolytic process Phase_0_2 4 GO:0016052 1.163932e-04 22.370370 0.28178090 4 13 carbohydrate catabolic process Phase_0_2 5 GO:0009185 1.604285e-04 20.121212 0.30345636 4 14 ribonucleoside diphosphate metabolic process Phase_0_2 6 GO:0009135 1.604285e-04 20.121212 0.30345636 4 14 purine nucleoside diphosphate metabolic process Phase_0_2 7 GO:0043436 2.085503e-04 5.450461 2.21089631 9 102 oxoacid metabolic process Phase_0_2 8 GO:0006165 2.153810e-04 18.280992 0.32513181 4 15 nucleoside diphosphate phosphorylation Phase_0_2 9 GO:0051186 1.523968e-03 7.114211 0.88680352 5 42 cofactor metabolic process Phase_0_2 what am I suppose to do, If I want to retrieve the geneIDs associated with each GOterms. The other information about params is params.bp.Phase_0_2<-GSEAGOHyperGParams(name="P.chabaudi",geneSetCollection=gsc,geneIds=Phase_0_2 ,universeGeneIds=universe,ontology="BP",pvalueCutoff=0.05,conditional=TRUE, testDirection="over") Looking forward to hear from you. With best regards, Amit -- Amit Kumar Subudhi, PhD Post Doctoral Research Scientist, Pathogen Genomics Group, Division of Biological and Environmental Sciences and Engineering, Level 4, 4326-WS10, Building 2, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia, Phone: (+966 12) 808 0614 <+966%2012%20808%200614>, Mobile: (+966) 5 40375986, Email Address: amit.subu...@kaust.edu.sa -- Amit Kumar Subudhi, PhD Post Doctoral Research Scientist, Pathogen Genomics Group, Division of Biological and Environmental Sciences and Engineering, Level 4, 4326-WS10, Building 2, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia, Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986, Email Address: amit.subu...@kaust.edu.sa [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel