Dear all,
I'm having some trouble fetching flanking regions for a gene from the
Ensembl Biomart:

library(biomaRt)
ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl",
      host="www.ensembl.org", path="/biomart/martservice")

attrs <- c("ensembl_gene_id", "upstream_flank")
gene_ann <- getBM(attributes=attrs,
filters=list(ensembl_gene_id="ENSG00000165702", upstream_flank=100),
mart=ensembl, checkFilters=F)
gene_ann

(here's a Gist: https://gist.github.com/jergosh/8159092)

I also tried passing the parameters differently but it doesn't make any
difference:

gene_ann <- getBM(attributes=attrs, filters=c("ensembl_gene_id",
"upstream_flank"), values=list(ensembl_gene_id="ENSG00000165702",
upstream_flank=100), mart=ensembl, checkFilters=F)

Am I doing something wrong?

Best,
Greg

-- 
Greg Slodkowicz
PhD student, Nick Goldman group
European Bioinformatics Institute (EMBL-EBI)

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