I am trying to calculate my own substitution matrix from a multiple sequence alignment. In one of the steps, I need a function that will calculate the number of times each residue pair shows up and the total number of ungapped pair slots. The code is difficult to understand without context, but I think my problem is with syntax, so if anyone has any idea why it's returning 0, it would help a lot.

0 is the initial value of the variable, so I think my code is not even entering the loops for some reason

    ResiduePairCalculator = function(combination_alignmentmatrix, aa_pairs) 

  {

  totalpaircount=0
  for(i in 1:ncol(combination_alignmentmatrix))
  {
    list_1=strsplit(combination_alignmentmatrix[1,i],split="")
    list_2=strsplit(combination_alignmentmatrix[2,i],split="")

      for(j in 1:length(list_1))
      {
          if((list_1[[j]]!="-") && (list_2[[j]]!="-"))
           {
            totalpaircount=totalpaircount+1

              for(k in 1:ncol(aa_pairs))
              {
                pair=paste(aa_pairs[1,k] , aa_pairs[2,k], sep = "")
                match1=paste(list_1[[j]],list_2[[j]], sep = "")
                match2=paste(list_2[[j]],list_1[[j]], sep = "")

                  if((pair==match1) || (pair==match2))
                  {
                    aa_pairs[3,k]=aa_pairs[3,k]+1
                    break
                  }
              }

            }
      }

  }
  return(totalpaircount)
}