This function converts a DNAStringSet
into an
seqinr
alignment
.
dnastring2aln(dna)
DNAStringSet
[mandatory]
An object of class alignment
which is a list with the
following components:
nb
the number of aligned sequences
nam
a vector of strings containing the names of the aligned
sequences
seq
a vector of strings containing the aligned sequences
com
a vector of strings containing the commentaries for each sequence
or NA
if there are no comments
## 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"