[BioC] where is the "getHomolog" function in biomaRt?

Marc Carlson mcarlson at fhcrc.org
Wed Mar 24 18:22:51 CET 2010

You could also use the inparanoid packages which provide mappings based
on data generated by the inparanoid algorithm.

# Lets suppose you started with the platform hgu95av2.db
# And had the following ids:
ids = c("1000_at","1001_at","1002_f_at","1003_s_at","1004_at" ,"1005_at")

# You would 1st want to get the entrez gene IDs (you need some sort of
universal gene ID for the next step)
EGIDs = mget(ids, hgu95av2ENTREZID, ifnotfound=NA)

# Then you could use the  idConverter function to convert from human to
mouse like this
result = idConverter(EGIDs, srcSpecies="HOMSA",
destSpecies="MUSMU",srcIDType="EG", destIDType="EG")

Does that help?


On 03/24/2010 09:27 AM, zrl wrote:
> Dear list,
> After asking how to do cross specices annotation. I tried BiomaRt, and
> find there is direct function "getHomolog" described in its manual to
> do this.
> But when I try to use it, it gave me the error:
> "Error: could not find function "getHomolog"
> Could anyone explain this to me? where should I found a version with
> this fucntion? Thanks.
> -Roger
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