[BioC] Mapping onto KO numbers (KEGG Orthology)

[James W. MacDonald]

Hi Alla,

Alla Bulashevska wrote:
> Dear Bioconductor users, 
> i have RefSeq gene descriptions and also UniProt
> identifiers.
> How can i map this onto KO numbers (KEGG Orthology), e.g.
> K03120 ?

I would use the org.Xx.eg.db package for your organism. Here is an 
example using the human package.

First convert UniProt IDs to Entrez Gene IDs

egs <- mget(<UniProt IDs>, revmap(org.Hs.eg.dbUNIPROT))

you should check the resulting list for any missing or duplicate values 
and deal with those in whatever manner you find useful. You then need to 
convert to a character vector using e.g., unlist()

Now convert Entrez Gene IDs to KEGG IDs

kegg <- mget(<Entrez Gene ID vector>, org.Hs.egPATH)

again, you may need to deal with duplicates.

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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