[BioC] query BiomaRt for the coordinates of the coding regions within individual exons?

Paul Shannon 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",  
"exon_chrom_end", "strand")
   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  
boundary coordinates?


  - Paul

More information about the Bioconductor mailing list