On Fri, Jul 17, 2009 at 12:07 AM, LiGang <luzifer.li@gmail.com> wrote:

> 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?
>

This type of query does not seem to be supported by the UCSC Table Browser.
As suggested by another poster, you could use their MySQL server. A
high-level interface to the UCSC database would be nice. I'm just not sure
if it falls within the scope of rtracklayer. The original goal of the
project was to represent tracks in R and interact with genome browsers. The
table browser interface was added for downloading tracks and we supported
arbitrary tables as well, because we got it almost for free. Something like
biomaRt for UCSC might belong in its own package. Discussion welcome.

Thanks,
Michael


>
> thanks!
>
> LiGang
>
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