[BioC] help with protein IPI annotation mappings

[Steffen Durinck]

Hi Mark,

I don't have an IPI id to test this but biomaRt should be able to do 
what you want.
Here's how:

library(biomaRt)
ipiID = c("your","list","of","IPI","IDs")
ensembl=useMart("ensembl", dataset="rnorvegicus_gene_ensembl")
getBM(attributes=c("ipi","entezgene"), filters="ipi", values=ipiID, 
mart=ensembl)

you could probably make the result of the query a little cleaner by:

getBM(attributes=c("ipi","entezgene"), filters=c("ipi","with_ipi"), 
values=list(ids=ipiID,""), mart=ensembl)

best,
Steffen



Kimpel, Mark William wrote:
> I need to map a list of rat International Protein Index accession ids to
> EntrezGene. The proteins have been identified using mass spectroscopy
> and thus do not necessarily correspond to any particular affy chipset.
> How would I do this in BioC? Can biomaRt handle this?
>
>  
>
> Thanks,
>
> Mark
>
>  
>
> Mark W. Kimpel MD 
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
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