msarc (version 1.3.2)

msarc.findGOterms: Map UniProt Ids to GO Terms

Description

Maps UniProt accession ids to the (multiple) GO terms they are associated with, and adds the map to the msarc object. Any given accession will most likely be associated with multiple GO terms.

Usage

msarc.findGOterms(msarc,eg2uniprot=org.Hs.eg.db::org.Hs.egUNIPROT,
                  eg2go=org.Hs.eg.db::org.Hs.egGO,minCount=10)

Arguments

msarc

the msarc object to add GO terms to.

eg2uniprot

an AnnDbBimap mapping Entrez gene IDs to Uniprot IDs.

eg2go

an AnnDbBimap mapping Entrez gene IDs to GO categories.

minCount

GO categories with fewer than minCount members in the UniProt IDs associated with this object will be discarded from the set of "interesting" categories.

Value

• the modified msarc object.

Details

The eg2uniprot and eg2go tables can be found in the annotation packages for various species. For example, the human and mouse packages are org.Hs.eg.db and org.Mm.eg.db, respectively.

This function is a bit slow.

References

The Gene Ontology Consortium, "Gene Ontology: tool for the unification of biology". Nature Genetics 25:25-29 (2000)

Examples

# Load a data set from a mass spec experiment
data(sample_subtracted,package="msarc")

# run the mapping stage
sample_go <- msarc.findGOterms(sample_subtracted)
data(sample_goterms,package="msarc")