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2001 Oct 06
0
calculating DNA mismatch distributions for large populations
...the
freqencies of sequence indices may total many thousands (often
30,000).
Right now, I am trying the following approach:
1) I create a 'distance matrix' of mismatches. I have been calculating
the mismatches using the following approach (states() creates a
list of two vectors: sl$aindex==indices and sl$state==sequences)
sl<-states(lnum,Rland);
rmat<-matrix(0,nrow=length(sl[[1]]),ncol=length(sl[[1]]));
for (i in 1:length(sl[[1]]))
for (j in i:length(sl[[1]]))
{
if (i!=j)
{...