Hi Paul, So to use what I just showed you to answer your specific question you can do this: library(GO.db) MFTerms <- Term(GOTERM[Ontology(GOTERM)=="MF"]) The GOTERM mapping from the GO.db package gives you all the terms from GO. So here I just subset that to be only the set that is in the "MF" ontology using the trick that I showed you before. Then you only need to call Term to get a vector of GO terms that are only from MF and where the names are the GOIDs. I used Term here, but really you could have used GOID, Definition, or Ontology as they all return a vector where the names *are* the GOIDs. The help page for Ontology will also show you how to use Term, GOID, Definition and related functions. Marc On 01/11/2011 01:49 PM, Paul Rigor wrote: > Hi Marc, > Actually, how to I obtain all of the GO IDs for a particular ontology? > Ideally, something like > > MFids = getGOIds(GOdb, ontology="MF") > > Thanks, > Paul > > > On Mon, Jan 10, 2011 at 11:57 AM, Marc Carlson <mcarlson@fhcrc.org> <mailto:mcarlson@fhcrc.org>> wrote: > > Hi Paul, > > Not completely sure what you are asking as you didn't give us a > concrete > example. So here is a rudimentary guess: > If I have a bunch of GO IDs in some vector: > > foo = c('GO:0008150','GO:0005576','GO:0003674') > > Then, I can get rid of the ones that are not of the "MF" ontology > (as an > example) by using the Ontology helper function from AnnotationDbi > in an > expression like this: > > > foo[Ontology(foo)=="MF"] > > > Hope that helps, > > > Marc > > > > > On 01/08/2011 11:29 PM, Paul Rigor wrote: > > Hi, > > > > I'm using topGO and I'm trying to obtain subsets of the three > ontologies. > > How do I go about obtaining just the GO terms associated with > MF, BP, or CC? > > > > I'm comparing raw counts from my experimental data (with separate > > enrichments per ontology) versus the background (for each of the > > ontologies). > > > > Thank you, > > Paul > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto: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]]