[BioC] Annotated a snp list to find where these snp are located.
Valerie Obenchain
vobencha at fhcrc.org
Thu Apr 11 00:41:15 CEST 2013
Hello,
The seqlevels (chromosome names) in the txdb and SNPlocs packages don't
match.
> rsID <- c("rs1929842", "rs10448261", "rs16942913", "rs9530156")
> SNPs.gr <- rsidsToGRanges(rsID)
> seqlevels(SNPs.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 <- 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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