[BioC] can you get end position information from org.Hs.eg

[Martin Morgan]

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
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 at post.harvard.edu> writes:

> I've been exploring the 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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