[BioC] overlapping genes with biomart

Elizabeth Purdom epurdom at stat.berkeley.edu
Thu Oct 16 01:03:31 CEST 2008


My understanding of the filters in biomaRt "start" and "end" is that 
they correspond to "start>=..." and "end<=..." so if I call

ens <- 
= 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?


More information about the Bioconductor mailing list