[BioC] SNP ID mapping with Oligo package

Solip [guest] guest at bioconductor.org
Mon Jun 2 18:13:20 CEST 2014

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 :)

 -- output of sessionInfo(): 

con <- db(pd.genomewidesnp.6);
ids_All <- dbGetQuery(con, "select man_fsetid from featureSet limit 906600;");
Info_All_add <- dbGetQuery(con, paste("select man_fsetid, dbsnp_rs_id, chrom, physical_pos, cytoband, allele_a, allele_b, gene_assoc 
from featureSet where man_fsetid in ('", paste(ids_All[,1], collapse="','"), "');", sep = ""));

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list