[BioC] SNP annotation in R
Ina Hoeschele
inah at vbi.vt.edu
Tue Jun 18 22:47:25 CEST 2013
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'
More information about the Bioconductor
mailing list