[BioC] How to find SNP names

[Hervé Pagès]

Hi Kay,

Kay Jaja wrote:
> If I have a list of SNPs Ref ID and I want to get the rs# for these SNPs, is there an R package that can help me find the SNP name for each corresponding SNPRefID. 
> I am  using SNPlocs.Hsapiens.dbSNP.20080617 package to find the SNP locations for Homo sapiens.
>  

If "SNP Red ID" stands for "RefSNP id", then I think there is actually
no difference between a SNP Ref ID and an rs#. My understanding is that
rs# is just short for "RefSNP id". This comes from the fact that all
RefSNP ids start with rs e.g. rs3894.

Note that the SNPlocs package strongly rely on this assumption because the
first column of the data frame you get with getSNPlocs("chrY") is named
"RefSNP_id" but it actually comes from the rs# field found in the ASN1_flat
files used to build those packages, and the "rs" prefix was dropped:

   > library(SNPlocs.Hsapiens.dbSNP.20090506)
   > chrY_snps <- getSNPlocs("chrY")
   > chrY_snps[1:10, ]
      RefSNP_id alleles_as_ambig     loc
   1   71201341                M 3189675
   2   71201342                R 3189731
   3   71201343                Y 3189757
   4   71201344                M 3189796
   5   71201345                W 3189856
   6    2534929                R 3190368
   7    2534930                R 3190405
   8    2534931                S 3190428
   9   56360280                W 3190617
   10  13304132                K 3191235

So the full ids are in fact:

   paste("rs", chrY_snps$RefSNP_id, sep="")

Cheers,
H.


> Your help is greatly appreciated
> 
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-- 
Hervé Pagès

Program in Computational Biology
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