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On Tue, Apr 11, 2017 at 8:32 AM, amit kumar subudhi <amit4h...@gmail.com> wrote: > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel