[BioC] query BiomaRt for the coordinates of the coding regions within individual exons?
pshannon at systemsbiology.org
Fri May 15 22:55:19 CEST 2009
I use BiomaRt to build a table of the coordinates of all the exons in
a gene transcript:
colnames = c ("ensembl_exon_id", "rank", "exon_chrom_start",
queryFields = 'entrezgene'
queryValues = geneID
tbl.exons = getBM (colnames, queryFields, queryValues,
Since not all bases in an exon (even interior exons) are in fact
coding, I now discover that I actually want the coordinates of the
coding regions within each of the exons, not just the exon
boundaries. Sometimes, maybe often (except for 3' and 5' UTRs) these
coordinates are the same.
Can anyone tell me how to query BiomaRt for the per-exon coding
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