Ina Hoeschele | 18 Jun 22:47 2013
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SNP annotation in R

Hi,
  I am interested in annotating lists of SNPs in R, mostly I am interested in finding the gene a SNP is located in
and for intergenic SNPs which genes are close by. I found this code that wsa developed with the help of
Valerie Obenchain:
http://adairama.wordpress.com/2013/02/15/functionally-annotate-snps-and-indels-in-bioconductor/
However, when I adapted this code to my problem I got the error message below. Can someone please give me a hint?
Thanks, Ina

input <- SNP.map.retain[SNPs,1:3]
rownames(input) <- NULL
colnames(input) <- c("rsid", "chr", "pos")
input
#       rsid chr      pos
#1  rs661761   1 30618672
#2 rs3754508   1 17255474
#3 rs6426403   1  4169394
#4  rs228727   1  7770423
#5 rs1635592   1 17535994
target <- with(input,
                GRanges( seqnames = Rle(chr),
                         ranges   = IRanges(pos, end=pos, names=rsid),
                         strand   = Rle(strand("*")) ) )
target
#GRanges with 5 ranges and 0 metadata columns:
#            seqnames               ranges strand
#               <Rle>            <IRanges>  <Rle>
#   rs661761        1 [30618672, 30618672]      *
#  rs3754508        1 [17255474, 17255474]      *
#  rs6426403        1 [ 4169394,  4169394]      *
#   rs228727        1 [ 7770423,  7770423]      *
#  rs1635592        1 [17535994, 17535994]      *
#  ---
#  seqlengths:
#    1
#   NA

loc <- locateVariants(target, 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'

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