R help - Aug 2010 - incrementing matrix elements more efficiently

I need to increment cells of a matrix (collusionM).  The indexes to increment
are in an index (matchIndex). This is some of the code

	for (j in 1:(rows-1)) matchIndex[[j]] <- which(mx[j]==mx)

	for (j in 1:(rows-1)) collisionM[j,matchIndex[[j]]] <-
collisionM[j,matchIndex[[j]]] + 1

I could put them in the same loop but this is slower.  The first for statement
is fine.  It finds the matches and creates a list of the matches.  The second is
too slow, it increments the sparse matrix elements.

Let me know if I need to put in more complete code to make this understandable.



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I need to increment cells of a matrix (collusionM).  The indexes to increment
are in an index (matchIndex). This is sample  code

   library(seqinr)
   library(Matrix)
   x <- "abcabcabc"
   mx <- s2c(x)
   collisionM <- Matrix(0,nrow=10, ncol=10, sparse=TRUE)
   matchIndex <- list()
   rows <- length(mx)
   for (j in 1:(rows)) matchIndex[[j]] <- which(mx[j]==mx)
   for (j in 1:(rows)) collisionM[j,matchIndex[[j]]] <-
collisionM[j,matchIndex[[j]]] + 1

  Works fine, except with my data (rows=32000) it is too slow.  The problem is
the second for loop, where it increments the index of the sparse matrix; this
needs to be rewritten so it is more efficient.  Any ideas?