[BioC] Annotated a snp list to find where these snp are located.

Fabrice Tourre fabrice.ciup at gmail.com
Thu Apr 11 00:16:47 CEST 2013


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 <- locateVariants(SNPs.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.



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