Transitions in R redux

April 28, 2010

(This article was first published on The Praise of Insects, and kindly contributed to R-bloggers)

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!

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]){

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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