[BioC] overlapping genes with biomart
Elizabeth Purdom
epurdom at stat.berkeley.edu
Thu Oct 16 01:03:31 CEST 2008
Hello,
My understanding of the filters in biomaRt "start" and "end" is that
they correspond to "start>=..." and "end<=..." so if I call
ens <-
getBM(c("ensembl_gene_id","start_position","end_position","chromosome_name"),filters
= c("chromosome_name", "start", "end"), values = list(chromosome, x1,
x2), mart = biomart)
then I would get a return of all genes that completely lie between x1
and x2. What I would like is all genes that overlap that region. Ideally
I could do this by a filter that does "start<=x2" and "end>=x1" but that
inverted filter doesn't seem to be predefined. Is there a simple way to
invert the filter? Or am I missing something else obvious?
Thanks,
Elizabeth
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