[BioC] Gene location (Base pair number)

[Martin Morgan]

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

  org.Hs.egCHRLOC[[egid]]
  org.Hs.egCHRLOCEND[[egid]]

for many symbols, symids, one might

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

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

Martin

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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