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 :) [[alternative HTML version deleted]]

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 :) > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]