[BioC] biomaRt: using a list as values. confused...
durinck.steffen at gene.com
Thu Jun 9 18:12:59 CEST 2011
the combo filter chr + start + end is a special situation and is
interpreted as give me everything in between. It is porbably not well
documented but this however filter combo works only for a single
region at a time so your second example is correct there are only few
genes in your region on chr1.
An alternative which does work for multiple regions is to use the
chromosomal_region filter like:
"chromosome_name","start_position", "end_position", "strand", "band")
On Thu, Jun 9, 2011 at 8:49 AM, <J.delasHeras at ed.ac.uk> wrote:
> I'm trying to obtain information about genes within a number of regions
> defined by a chromosome name, start and end coordinates.
> I understand that the way to specify multiple filters to be used together (a
> set of chr+start+end) is to use a list for 'values'.
> This seems to work ok when I have more than one region (I tested it using
> two regions first, before doing the proper search for >1000), but if I were
> to specify just one region, it does not work... and I'm wondering how I
> would do it in that case.
> ensembl = useMart("ENSEMBL_MART_ENSEMBL",
> chrom<-c("1", "2")
> chr.start<-c(11401198, 86460656)
> chr.stop<-c(11694590, 86663869)
> attributes<-c("hgnc_symbol", "entrezgene", "chromosome_name",
> "start_position", "end_position", "strand", "band")
> # extract both regions at once:
> #this works, returning 1939 rows of data, the first 1198 with chr1
> #corresponding to teh first region, and the rest with chr2 to teh second.
> #but how does one retrieve the data for just ONE region?
> # try this:
> # it only returns one gene!!! (in two rows)
> so, when I just want to do a single search with multiple filters, how would
> I specify the values?
> Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
> The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090
> Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
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