An R function for fetching SNP annotations?
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6.1 years ago
kindlychung ▴ 60

Is there an R function in any existing package that allows me to do something like:

annotate("rs34121", build = hg19)

and returns either of these:

  • gene name, if the SNP is inside a gene
  • gene1/gene2, if the SNP is between gene1 and gene2 ?
SNP annotation r • 1.9k views
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3
Entering edit mode
6.1 years ago
poisonAlien ★ 3.0k
source("http://bioconductor.org/biocLite.R")
biocLite("FDb.UCSC.snp137common.hg19")

snp137 = features(FDb.UCSC.snp137common.hg19)
snp137['rs34121']

 

It give you the position of rsid, but not sure about gene name.

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