Hi gang, I was wondering if there's anyway to obtain the adjacency list of matrix of the induced go graphs, eg, the graphs generated by the printGraph function? Thanks, Paul On Wed, Dec 22, 2010 at 3:21 AM, Paul Rigor <pryce@ucla.edu> wrote: > Thank you, this works quite well. I wish topGO had a prettier way of > printing out the results similar to GOstats, though. > > Cheers, > Paul > > > On Sun, Dec 19, 2010 at 2:59 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > >> Hi Paul, >> >> >> On 12/17/10 13:41, Paul Rigor wrote: >> >>> Hello, >>> >>> So I'm working on extracting IDs from a topGO result object. I have a >>> list of terms ranked by p values (using classic fisher test). However, >>> does the result object >>> contain indices to the original list of gene ids per go term? The >>> documentation was a bit unclear. >>> >>> Using the printGenes function and specifying the top ranked GO terms, >>> I'd like to only pull the genes from my gene list, not from the entire >>> GO annotation table, which seems to be the default behavior for this >>> function. >>> >>> >> Using the example from the topGO vignette, >> >> sampleGOdata <- new("topGOdata", description = "Simple session", >> ontology = "BP", >> allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, annot >> = annFUN.db, >> affyLib = affyLib) >> >> resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic >> = "fisher") >> >> >> Create a map of geneIDs to GO terms, >> >> ann.genes <- genesInTerm(sampleGOdata) >> str(ann.genes) >> >> Select a few GO terms from the Fisher analysis (you could sort these first >> or ...), >> >> fisher.go <- names(score(resultFisher))[1:5] >> fisher.ann.genes <- genesInTerm(sampleGOdata, whichGO=fisher.go) >> fisher.ann.genes >> >> The fisher.ann.genes list give you the gene ID / GO term mapping subset >> on the GO terms from the Fisher analysis. You can also use printGenes on >> this subset of GO terms, >> >> ft <- printGenes(sampleGOdata, whichTerms=fisher.go, >> chip="hgu95av2.db") >> >> >> >> Valerie >> >> Thanks, >>> Paul >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> > [[alternative HTML version deleted]]