Hi Boel,

I didn't try your code, but probably you are not getting anything because
there is no gene that starts and ends exactly in the positions you have
specified in your filters. I had to do  something similar and what I did was
to download all the ensembl_gene_ids for the chromosomes together with the
start and end information and then I made a query in mysql, to find the ones
overlaping with my regions of interest, this is fast, but needs two steps.
With kind regards,
Andreia

On Mon, Jan 18, 2010 at 5:28 PM, Boel Brynedal <Boel.Brynedal@ki.se> wrote:

> Dear List,
>
> I have long lists of genomic regions (chr;start;end) where a given event
> has taken place. These regions can be an exon, an intronic region, or
> similar.  Most (all) of these events have taken place within the
> boundaries of genes, and I would like to retrieve the gene names
> (ensemble ID).
>
> I've tried to use biomaRt:
> >
>
> getBM(attributes=c("ensembl_gene_id"),filter=c("chromosome_name","start","end"),
> values=list(10,17317394,17317851), mart=ensembl)
> [1] ensembl_gene_id
> <0 rows> (or 0-length row.names)
>
> But since no whole GENE is within these boundaries, I get nothing. i've
> also tried asking for "ensembl_exon_id" when looking at exon events (not
> all of them are of that kind however), and this generally results in a
> long list of exon IDs (because one exon can be part of several
> transcripts).
>
> I would appreciate any ideas of how this could be done in a better way.
>
> Thank you!
>
> Boel
>
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-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

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