msarc.findGOterms: Map UniProt Ids to GO Terms

In msarc: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments

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.

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.

Value

the modified msarc object.

Note

It is normal if a few UniProt accessions cannot be mapped to Entrez IDs, or from there to GO terms. The unmapped accessions will be listed after the mapping is complete, with the message "missing UniProt IDs: ...".

Author(s)

Gord Brown

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
## Not run: sample_go <- msarc.findGOterms(sample_subtracted)

msarc documentation built on May 30, 2017, 12:53 a.m.