[BioC] Querying dbSNP
stvjc at channing.harvard.edu
Mon Oct 19 23:02:10 CEST 2009
It may also be noteworthy that the SNPlocs.Hsapiens.dbSNP.20090506
package has location and allele information for build 130 dbSNP
entries. A substantial quantity of SNP-related metadata is present in
the pd.genomewidesnp.6 annotation package.
'Queries' to dbSNP of a more general nature could probably be
programmed using various web services support packages in R/bioc. If
you describe a compelling use case, code might be written to solve it.
On Mon, Oct 19, 2009 at 4:30 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Sharon,
> It's not clear to me from your email what you intend to do, but I know
> that some dbSNP data is available as a UCSC track and should therefore
> be obtainable by using the rtracklayer package.
> Sharon wrote:
>> Dear All,
>> Is there any tool in Bioconductor to query dbSNP? I know that (correct me,
>> if I am wrong) biomaRt is primarily for Ensemble.
>> Thanks in advance.
>> Kind regards,
>> [[alternative HTML version deleted]]
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