Dear list, I want to annotate a snp list to find where these snp are located. I used fellow code. But there is a error. Or do you have other solution for this purpose? rsID <- c("rs1929842", "rs10448261", "rs16942913", "rs9530156", "rs9543238", "rs3757718", "rs17564689","rs10167958", "rs13444824", "rs10777752", "rs10072700", "rs10842099","rs11024171", "rs797516", "rs2046545", "rs12996997", "rs6135128","rs2143072", "rs12585354" ,"rs797515", "rs17073211", "rs10496454","rs17197639", "rs4704128", "rs2143071", "rs3748997", "rs2292100") library(Homo.sapiens) library(VariantAnnotation) library("SNPlocs.Hsapiens.dbSNP.20120608") SNPs.gr <- rsidsToGRanges(rsID) vars <- locateVariantsSNPs.gr, TxDb.Hsapiens.UCSC.hg19.knownGene, AllVariants()) Error in .mk_isActiveSeqReplacementValue(x, value) : the names of the supplied 'isActiveSeq' must match the names of the current 'isActiveSeq' unlist(mget(vars$GENEID, org.Hs.egSYMBOL)) Thank you.

Hello, The seqlevels (chromosome names) in the txdb and SNPlocs packages don't match. > rsID <- c("rs1929842", "rs10448261", "rs16942913", "rs9530156") > SNPs.gr <- rsidsToGRanges(rsID) > seqlevelsSNPs.gr) [1] "ch1" "ch2" "ch3" "ch4" "ch5" "ch6" "ch7" "ch8" "ch9" ... > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > seqlevels(txdb) [1] "chr1" "chr2" "chr3" ... You can rename seqlevels in your GRanges using renameSeqlevels(), paste(), or seqlevels()<-. See any of ?locateVariants, ?renameSeqlevels, ?seqlevels for examples and details. Valerie On 04/10/2013 03:16 PM, Fabrice Tourre wrote: > Dear list, > I want to annotate a snp list to find where these snp are located. I > used fellow code. But there is a error. Or do you have other solution > for this purpose? > > rsID <- c("rs1929842", "rs10448261", "rs16942913", "rs9530156", > "rs9543238", "rs3757718", "rs17564689","rs10167958", "rs13444824", > "rs10777752", "rs10072700", "rs10842099","rs11024171", "rs797516", > "rs2046545", "rs12996997", "rs6135128","rs2143072", "rs12585354" > ,"rs797515", "rs17073211", "rs10496454","rs17197639", "rs4704128", > "rs2143071", "rs3748997", "rs2292100") > library(Homo.sapiens) > library(VariantAnnotation) > library("SNPlocs.Hsapiens.dbSNP.20120608") > SNPs.gr <- rsidsToGRanges(rsID) > vars <- locateVariantsSNPs.gr, TxDb.Hsapiens.UCSC.hg19.knownGene, > AllVariants()) > > Error in .mk_isActiveSeqReplacementValue(x, value) : > the names of the supplied 'isActiveSeq' must match the names of the > current 'isActiveSeq' > > unlist(mget(vars$GENEID, org.Hs.egSYMBOL)) > > > Thank you. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >