[BioC] biomaRt and HapMap

[Steffen Durinck]

Hi Deidre,

It looks like there is some issue with HapMap in the BioMart central
repository.  You might want to do your query using the hapmap web
interface at:

http://hapmap.ncbi.nlm.nih.gov/biomart/martview/

Cheers,
Steffen

On Fri, Jul 22, 2011 at 5:58 AM, Deidre <deidre.krupp at duke.edu> wrote:
> I need to get SNP data from HapMap via biomaRt, but am having trouble
> getting any results from any query of the hapmap_rel27 dataset.  For
> example, both of the following:
>
> HM <- useMart("HapMap_rel27","hm27_variation_ceu")
> ceu <- getBM(
> c("chrom","start","strand","marker1"),
> filters=c("chrom"), values="chr22",HM)
> )
>
> hapmap <- useMart("HapMap_rel27", dataset="hm27_variation_yri")
> yri <-
> getBM(c("chrom","start","alleles","ref_allele","ref_allele_freq","other_allele_freq",filters=c("chrom","coding_nonsynon"),values=list("chr19",TRUE),mart=hapmap)
>
> result in an empty table such as:
>
>  > head(yri)
> [1] chrom             start             alleles
> ref_allele        ref_allele_freq   other_allele_freq
> <0 rows> (or 0-length row.names)
>
> I've tried with both biomaRt 2.8.1 and 2.9.2.  Queries to marts ensembl
> or snp work as expected.  Am I missing a detail in my queries to HapMap,
> or is there an issue with the mart?
>
> Regards,
> Deidre
>
>
>  > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1251  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_united States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] stats    graphics  grDevices utils    datasets methods  base
>
> other attached packages:
> [1] biomaRt_2.9.2
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.6-6.1 tools_2.13.0 XML_3.4-0.2
>
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>
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