[BioC] subset ontology from entire GO db using topGO

[Marc Carlson]

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 at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>