Dear Solip -- your question is not particularly clear.  You seem to be
working with GWAS catalog.
There is a package

> library(gwascat)
> gwr = as(gwrngs, "GRanges")
> gwr[which(gwr$SNPs=="rs7023329"), c("Disease.Trait", "SNPs", "PUBMEDID")]
GRanges with 2 ranges and 3 metadata columns:
      seqnames               ranges strand | Disease.Trait        SNPs
         <Rle>            <IRanges>  <Rle> |   <character> <character>
  [1]     chr9 [21816528, 21816528]      * |      Melanoma   rs7023329
  [2]     chr9 [21816528, 21816528]      * |      Melanoma   rs7023329
       PUBMEDID
      <integer>
  [1]  21983787
  [2]  19578364
  ---
  seqlengths:
        chr1      chr2      chr3      chr4 ...     chr21     chr22      chrX
   249250621 243199373 198022430 191154276 ...  48129895  51304566 155270560


This gives the location asserted by NHGRI catalog for one of the SNP you
ask about.  You
can use SNPlocs.*, biomaRt, and other resources, to obtain additional
information about
SNP locations.

Sincerely,
Vince Carey


On Mon, Jun 2, 2014 at 12:08 PM, Solip Park <imagineyd@gmail.com> wrote:

> Hello :)
>
> I want to map GWAS SNPs (from http://www.genome.gov/gwastudies) to SNP IDs
> using R package (with pd.genomewidesnp.6).
>
> >From R package with this function (dbGetQuery), I could get all SNPs IDs
> information (906600 SNPs). But I found something strange. Because hundreds
> SNPs from GWAS couldn't map to SNP IDs (6.0 Aﬀymetrix arrays IDs, e.g.,
> SNP_A-8682034).
>
> For example, I couldn't find these SNPs with R package: rs7023329 or
> rs7412746.
>
> Somebody can help me?
>
> Many thanks :)
>
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