2009/1/29 Patrick Aboyoun <paboy...@fhcrc.org>:
> Hadassa,
> You may want to check out the snpMatrix package in Bioconductor
>
> http://bioconductor.org/packages/2.3/bioc/html/snpMatrix.html
> http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
>
> It contains classes that manage this type of information and should minimize
> your coding effort.
It's not that much effort - this code turns all ties into 1s:
snp2maf=function(m){
m=toupper(m)
return(t(apply(m,1,makeBin)))
}
makeBin = function(chars){
tc = table(chars)
maxV = names(tc[tc==max(tc)])
matches = match(chars,maxV)
r=as.integer(!is.na(matches))
return(r)
}
then:
> m
[,1] [,2] [,3] [,4] [,5]
[1,] "t" "g" "g" "g" "t"
[2,] "a" "G" "a" "C" "c"
[3,] "A" "T" "c" "c" "C"
[4,] "g" "T" "c" "A" "C"
[5,] "G" "C" "G" "g" "G"
[6,] "G" "t" "T" "a" "C"
[7,] "A" "G" "T" "g" "T"
[8,] "T" "a" "C" "a" "T"
[9,] "t" "g" "g" "c" "T"
[10,] "A" "t" "t" "c" "A"
> snp2maf(m)
[,1] [,2] [,3] [,4] [,5]
[1,] 0 1 1 1 0
[2,] 1 0 1 1 1
[3,] 0 0 1 1 1
[4,] 0 0 1 0 1
[5,] 1 0 1 1 1
[6,] 0 1 1 0 0
[7,] 0 1 1 1 1
[8,] 1 1 0 1 1
[9,] 1 1 1 0 1
[10,] 1 1 1 0 1
>
Barry
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