[SOLVED] Is there an R function that returns the alignment score of aligned DNA sequences?

Is there an R function that returns the alignment score of aligned DNA sequences?

I want to take two strings (DNA Sequences) and generate an alignment score. I found the DECIPHER package but that only let me generate the alignment, not the alignment score. I also tried using "Biostrings", but I was unable to generate the score.

Thanks for your help!

string1 <- "ACAGT"
string2 <- "CCAGTA"

I'm looking for something like this

t <- FunctionThatWouldReturnAlignmentScore(string1, string2)
print(t) # this returns 2

Solution

In Biostrings I did

> aln = pairwiseAlignment(pattern = c("succeed", "precede"), subject = "supersede")
> aln
Global PairwiseAlignmentsSingleSubject (1 of 2)
pattern: succ--eed
subject: supersede
score: -33.99738
> score(aln)
[1] -33.99738 -25.11710

by following the vignette on pairwise sequence alignment linked from the page above.

I also discovered

> dist = stringDist(DNAStringSet(c(string1, string2)))
> methods(class=class(dist))
[1] as.matrix   coerce      format      initialize  labels      print
[7] show        slotsFromS3
see '?methods' for accessing help and source code
> as.matrix(dist)
  1 2
1 0 2
2 2 0