[R] incrementing matrix elements more efficiently

[david h shanabrook]

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?