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. Your help is greatly appreciated [[alternative HTML version deleted]]

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 > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319