[BioC] biomaRt-chromosomal positions

[P.A.C._t_Hoen at lumc.nl]

Dear BioC

I would like to use biomaRt to get entrez gene (or other) identifiers
for small tag sequences. I use the getFeature function for this. It
seems that it will retrieve the identifiers only when the chromosomal
region indicated spans at least the complete length of the transcript,
but not if the indicated chromosomal region contains only part of the
transcript sequence. Is there a way aroud here?

Code and sessionInfo:

library(RCurl)
library(biomaRt)
ensembl = useMart("ensembl")
ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
testgene <- getGene("66501", type = "entrezgene", mart = ensembl)
testgene
#  entrezgene  markersymbol
#description chromosome_name band strand start_position end_position
#1      66501 1700029H14Rik RIKEN cDNA 1700029H14 gene
#[Source:MarkerSymbol;Acc:MGI:1913751]               8   A2     -1
#13550710     13562382
#     ensembl_gene_id ensembl_transcript_id
#1 ENSMUSG00000031452    ENSMUST00000033830

#this works fine:
testfeatures = getFeature( type = "entrezgene", chromosome = "8", start
= "13550710", end = "13562382",mart=ensembl)
testfeatures
#  chromosome_name start_position end_position entrezgene
#1               8       13550710     13562382      66501

#this does  not work anymore
testfeatures = getFeature( type = "entrezgene", chromosome = "8", start
= "13550711", end = "13562381",mart=ensembl)
testfeatures
#NULL

#I would like to have a result from a small tag in a query like this:
testfeatures = getFeature( type = "entrezgene", chromosome = "8", start
= "13550741", end = "13550761",mart=ensembl)


sessionInfo()
----------------------
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "stats"     "graphics"  "grDevices" "datasets"  "utils"     "tcltk"
"methods"   "base"     

other attached packages:
 biomaRt    RCurl      XML     svIO   R2HTML   svMisc svSocket    svIDE 
"1.11.4"  "0.8-0"  "1.7-3"  "0.9-5"   "1.58"  "0.9-5"  "0.9-5"  "0.9-5"



Cheers,
Peter-Bram