Hello friends, I have list of 120 genes and associated SNPs information of a cancer and want to find selection pressure in specific population using SNP information from 1000 genome. To do that I need genotype information for SNPs present in those genes from 1000 genome. Hence, any sort of suggestion to retrieve such information in automated way from 1000 genome would be helpful. Regards, prashantha [[alternative HTML version deleted]]

there are various approaches if you have ALL.chr17.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz in current folder, the following code shows one way snpsInGene = function(gr, vcf, genotag="hg19", ...) { p = ScanVcfParam(which=gr, ,...) geno(readVcf(vcf, genome=genotag, param=p))$GT } library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb = TxDb.Hsapiens.UCSC.hg19.knownGene txg = transcriptsBy(txdb, by="gene") # # prepare for entrez gene 47 (ACLY) # acly.gr = reduce(txg$"47") seqlevelsacly.gr) = gsub("chr", "", seqlevelsacly.gr)) fn = "ALL.chr17.phase1_release_v3.20101123.snps_indels_svs.genotypes.v cf.gz" inacly = snpsInGene( acly.gr, fn, geno="GT", info=NA) > dim(inacly) [1] 545 1092 > inacly[1:5,1:5] HG00096 HG00097 HG00099 HG00100 HG00101 rs184327140 "0|0" "0|0" "0|0" "0|0" "0|0" rs146150856 "0|0" "0|0" "0|0" "0|0" "0|0" rs7713 "0|0" "1|0" "0|0" "0|0" "0|0" rs140162090 "0|0" "0|0" "0|0" "0|0" "0|0" rs189951396 "0|0" "0|0" "0|0" "0|0" "0|0" how to map from sample IDs to populations is another matter. this is a good use case so more infrastructure should probably be ready to hand. On Sat, Jul 20, 2013 at 8:21 AM, Prashantha Hebbar < prashantha.hebbar@yahoo.com> wrote: > Hello friends, > > I have list of 120 genes and > associated SNPs information of a cancer and want to find selection > pressure in specific population using SNP information from 1000 genome. > To do that I need genotype information for SNPs present in those genes > from 1000 genome. Hence, any sort of suggestion to retrieve such > information in automated way from 1000 genome would be helpful. > > Regards, > prashantha > > [[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]]