aln2dnastring

This function converts a seqinr alignment into an DNAStringSet.

aln2dnastring(aln)

Arguments

aln

seqinr alignment [mandatory]

Value

An object of class DNAStringSet

See also

as.alignment DNAStringSet

Author

Kristian K Ullrich

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
## convert into alignment
#dnastring2aln(cds1.cds2.aln)
cds1.cds2.aln |> dnastring2aln()
#> $nb
#> [1] 2
#> 
#> $nam
#> NULL
#> 
#> $seq
#> [1] "atgcaacattgc" "atg---cattgc"
#> 
#> $com
#> [1] NA
#> 
#> attr(,"class")
#> [1] "alignment"
## convert back into DNAStringSet
#aln2dnastring(dnastring2aln(cds1.cds2.aln))
cds1.cds2.aln |> dnastring2aln() |> aln2dnastring()
#> DNAStringSet object of length 2:
#>     width seq
#> [1]    12 ATGCAACATTGC
#> [2]    12 ATG---CATTGC