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> 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
> >
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> >
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