Question: Problem with a function iterating over a matrix in R

0

Pia •

**10**wrote: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)
}
```

No, all you can say is the the incrementing line is probably not being run. No statement can be made about the loop with just the return value.

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