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

On Wed, Oct 15, 2008 at 7:03 PM, Elizabeth Purdom <epurdom at="" stat.berkeley.edu=""> wrote: > 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","chromosom e_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? It is possibly easier to simply pull in all genes and then do the overlaps in R. You could also write raw SQL, but that will mean accessing the mysql server directly and either a temp table (not possible at ensembl) or multiple queries if you have more than one region. Sean