Sorry and thanks for the information. On 11 Apr 2017 6:00 p.m., "James W. MacDonald" <jmac...@uw.edu> wrote:
> This list is intended for discussions about package development, not > general queries. Please post that sort of question on the support site, > https://support.bioconductor.org > > 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> >> <+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