[BioC] problem about using 'rtracklayer' to retrieve chromosome position of SNPs

LiGang luzifer.li at gmail.com
Fri Jul 17 09:10:58 CEST 2009


Dear List,

using rtracklayer, it's possible to retrieve data with functions of
'ucscTableQuery' and 'getTable'.
however, these functions could only retrieve data given a genomic range.
For example, using following code could retrieve snps between 10000 to 20000
basepair on chromosome 2.

####======================
library(rtracklayer)
browserSession("UCSC")->session
ucscTableQuery(session, "snp129",GenomicRanges(10000,20000, 2))->todo
tableName(todo)<-"snp129"
getTable(todo)
####======================

my question is how to retrieve data using identifiers(names/accessions).
for example, is it possible to retrieve chromosome position given the rs number
of several SNPs, such as 
rs10003974
rs10087355
rs10075230
...

is there any function in 'rtracklayer' package can do this?

thanks!

LiGang



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