[BioC] biomaRt: using a list as values. confused...

[J.delasHeras at ed.ac.uk]

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.

Example:

library("biomaRt")
ensembl = useMart("ENSEMBL_MART_ENSEMBL",
    dataset="hsapiens_gene_ensembl",
    host="www.ensembl.org")

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:
getBM(attributes=attributes,
       filters=c("chromosome_name","start","end"),
       values=list(chrom,chr.start,chr.stop),mart=ensembl)
#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. Good.

#but how does one retrieve the data for just ONE region?
# try this:
getBM(attributes=attributes,
       filters=c("chromosome_name","start","end"),
       values=list(chrom[1],chr.start[1],chr.stop[1]),mart=ensembl)
# 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?

Jose

-- 
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
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