One kind of ugly solution
> d.f=data.frame(seq1, seq2, stringsAsFactors=FALSE)
> d.f[["nMismatch"]] <- with(d.f, {
+ m <- mapply("!=", strsplit(seq1, ""), strsplit(seq2, ""))
+ colSums(m)
+ })
Check out the Bioconductor Biostrings package, especially the version
available with the development version of R, for DNA string algorithms.
Martin
joseph wrote:
> Hello
> I have 2 columns of short sequences that I would like to compare and count
> the number of mismatches and record the number of mismatches in a new
> column. The sequences are part of a data frame that looks like this:
> seq1=c("CGGTGTAGAGGAAAAAAAGGAAACAGGAGTTC","CGGTGGTCAGTCTGGGACCTGGGCAGCAGGCT",
> "CGGGCCTCTCGGCCTGCAGCCCCCAACAGCCA")
> seq2=c("AGGTGTAGAGGAAAAAAAGGAAACAGGAGTTC","CAGTGGTCAGTCTGGGACCTGGGCATCAGGCT",
> "CGGGCCTCTCGGCCTGCAGCCCCCAACAGCCA")
> d.f=data.frame(seq1, seq2)
> thank you for your help
> Joseph
>
>
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>
>
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