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Previously, I shared with the world a function to create a pairwise matrix of the number of transitions and transversions between two DNA sequences. Klaus Schliep kindly pointed out the possibility of a bug in the function and offered a faster, more accurate version. Thanks Klaus!Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.
titv< -function(dat){
mat< -as.matrix(dat)
res< -matrix(NA, ncol=dim(mat)[1], nrow=dim(mat)[1], dimnames=list(x=names(dat), y=names(dat)))
for(i in 1:(dim(mat)[1] – 1)){
for(j in (i+1):dim(mat)[1]){
vec< -as.numeric(mat[i,])+as.numeric(mat[j,])-8
res[j,i]< -sum(!is.na(match(vec,c(200,56))))#Transitions
res[i,j]< -sum(!is.na(match(vec,c(152,168,88,104))))#Transversions
}
}
res
}
The previous version of the function considered the difference between an unknown base (coded as N) and a T as a transition. The new version does not detect this difference.
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