[BioC] Gene location (Base pair number)

Martin Morgan mtmorgan at fhcrc.org
Fri Jul 3 20:10:54 CEST 2009

Hi Tim --

One suggestion is to use the org.Hs.eg.db package. The 'eg' means that
the information is keyed off Entrez ids, so you need to map your SYMBOL
to EG

  egid = revmap(org.Hs.egSYMBOL)[["WNT16"]]

and then retrieve location information


for many symbols, symids, one might

  egids = mappedLkeys(revmap(org.Hs.egSYMBOL)[symids])

etc. Some book-keeping might be needed to ensure correct symid -> egid
-> CHRLOC mapping


Tim Smith wrote:
> Hi,
> I wanted the exact base pair locations for several genes (e.g. wnt16 in the human wnt pathway). Which bioconductor package should I use?
> thanks!
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