Thanks, that was what I was looking for.

Andrew

On Feb 19, 2008 7:11 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Andrew --
>
> I guess the thread you reference is about finding entrez ids when
> chromosome locations are known, whereas you're doing something
> different. I don't think the end positions are in the org.Hs.eg<http://org.hs.eg/>
> packages.
>
> One strategy is to use biomaRt, e.g.,
>
> > library(biomaRt)
> > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
> > getGene(c("1", "100"), listFilters(mart)[59, 1], mart=mart)
>  entrezgene hgnc_symbol
> 1          1        A1BG
> 2        100         ADA
>
>               description
> 1    Alpha-1B-glycoprotein precursor (Alpha-1-B glycoprotein).
> [Source:Uniprot/SWISSPROT;Acc:P04217]
> 2 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase).
> [Source:Uniprot/SWISSPROT;Acc:P00813]
>  chromosome_name   band strand start_position end_position ensembl_gene_id
> 1              19 q13.43     -1       63548356     63556669
> ENSG00000121410
> 2              20 q13.12     -1       42681578     42713795
> ENSG00000196839
>
> Martin
>
>
> "Andrew Yee" <yee@post.harvard.edu> writes:
>
> > I've been exploring the org.Hs.eg <http://org.hs.eg/> package.  I can
> see how you can get start
> > locations of genes from org.Hs.egCHRLOC, but how do you get the end
> location
> > for a given gene ID?  Apologies if this is obvious.  I've already looked
> > through the info here:
> >
> > https://stat.ethz.ch/pipermail/bioconductor/2007-December/020625.html
> >
> > and don't see this explicitly addressed.
> >
> > Thanks,
> > Andrew
> >
> >       [[alternative HTML version deleted]]
> >
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>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>

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