[BioC] Retrieving gene name where given genomic region is included.

Boel Brynedal Boel.Brynedal at ki.se
Mon Jan 18 18:28:26 CET 2010

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:
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!


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