Hi all, I've been successfully using the GOstats package for a while now to do testing for over-representation of GO terms. I'd also like to use it as a quick way to output all the GO terms that get tested. However, I can't get the GOHyperGResult object to output all the GO terms that it says it tested, it will only output those that are below the pvalueCutoff specified. Even when I raise the pvalueCutoff to 1 (max allowed value), I still can't get all the terms. Here's a reproducible example: > library(ALL) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(GOstats) Loading required package: Category Loading required package: AnnotationDbi Loading required package: graph Loading required package: DBI > library(hgu95av2.db) Loading required package: org.Hs.eg.db > > data(ALL, package = "ALL") > > > sel.IDs <- unique(unlist(mget(featureNames(ALL)[1:20],hgu95av2ENTREZID))) > uni.IDs <- unique(unlist(mget(featureNames(ALL),hgu95av2ENTREZID))) > > > params <- new("GOHyperGParams", geneIds=sel.IDs, universeGeneIds=uni.IDs, + annotation="hgu95av2.db",ontology="BP",pvalueCutoff=1, conditional=T, + testDirection="over") > > hgOver <- hyperGTest(params) > hgOver Gene to GO BP Conditional test for over-representation 356 GO BP ids tested (184 have p < 1) Selected gene set size: 18 Gene universe size: 7685 Annotation package: hgu95av2 > > dim(summary(hgOver)) [1] 184 7 As you can see, the hgOver object says that it tested 356 GO BP ids, but only 184 have p < 1, so the summary(hgOver) only has 184 rows. Is there any easy way to get all 356 GO terms out, along with their ExpCount, Count, Size, etc.? Thanks, Jenny > > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.3.5 hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 [4] GOstats_2.12.0 RSQLite_0.8-0 DBI_0.2-5 [7] graph_1.24.1 Category_2.12.0 AnnotationDbi_1.8.1 [10] ALL_1.4.7 Biobase_2.6.1 loaded via a namespace (and not attached): [1] annotate_1.24.0 genefilter_1.28.2 GSEABase_1.8.0 RBGL_1.22.0 [5] splines_2.10.1 survival_2.35-7 tools_2.10.1 XML_2.6-0 [9] xtable_1.5-6 > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu

Dear Jenny, It looks like the pvalue parameter in the summary of a hyperGTest is strict, so 184 have p<1 while the rest are exactly 1. A quick, brute force was to overcome this is to call the summary with a pvalue greater than one, > dim(summary(hgOver, pvalue=1.1)) [1] 356 7 A more elegant way is to inspect the content of the results: > slotNames(hgOver) [1] "goDag" "pvalue.order" "conditional" "annotation" [5] "geneIds" "testName" "pvalueCutoff" "testDirection" Tested GO ids are contained in the goDag slot, the nodes of which are the tested GO ids, so: >length(nodes((goDag(hgOver)))) [1] 356 > nodes((goDag(hgOver)))[1:3] GO:0000002 GO:0000018 GO:0000279 "GO:0000002" "GO:0000018" "GO:0000279" HTH. J. On 21/01/2010 16:33, Jenny Drnevich wrote: > Hi all, > > I've been successfully using the GOstats package for a while now to do > testing for over-representation of GO terms. I'd also like to use it as > a quick way to output all the GO terms that get tested. However, I can't > get the GOHyperGResult object to output all the GO terms that it says it > tested, it will only output those that are below the pvalueCutoff > specified. Even when I raise the pvalueCutoff to 1 (max allowed value), > I still can't get all the terms. Here's a reproducible example: > > > library(ALL) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > library(GOstats) > Loading required package: Category > Loading required package: AnnotationDbi > Loading required package: graph > Loading required package: DBI > > library(hgu95av2.db) > Loading required package: org.Hs.eg.db > > > > data(ALL, package = "ALL") > > > > > > sel.IDs <- > unique(unlist(mget(featureNames(ALL)[1:20],hgu95av2ENTREZID))) > > uni.IDs <- unique(unlist(mget(featureNames(ALL),hgu95av2ENTREZID))) > > > > > > params <- new("GOHyperGParams", geneIds=sel.IDs, > universeGeneIds=uni.IDs, > + annotation="hgu95av2.db",ontology="BP",pvalueCutoff=1, conditional=T, > + testDirection="over") > > > > hgOver <- hyperGTest(params) > > hgOver > Gene to GO BP Conditional test for over-representation > 356 GO BP ids tested (184 have p < 1) > Selected gene set size: 18 > Gene universe size: 7685 > Annotation package: hgu95av2 > > > > dim(summary(hgOver)) > [1] 184 7 > > As you can see, the hgOver object says that it tested 356 GO BP ids, but > only 184 have p < 1, so the summary(hgOver) only has 184 rows. Is there > any easy way to get all 356 GO terms out, along with their ExpCount, > Count, Size, etc.? > > Thanks, > Jenny > > > > > sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.3.5 hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 > [4] GOstats_2.12.0 RSQLite_0.8-0 DBI_0.2-5 > [7] graph_1.24.1 Category_2.12.0 AnnotationDbi_1.8.1 > [10] ALL_1.4.7 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] annotate_1.24.0 genefilter_1.28.2 GSEABase_1.8.0 RBGL_1.22.0 > [5] splines_2.10.1 survival_2.35-7 tools_2.10.1 XML_2.6-0 > [9] xtable_1.5-6 > > > > > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >