dnastring2codonmat: dnastring2codonmat

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

dnastring2codonmat

Description

This function converts a DNAStringSet into a codon matrix.

Usage

dnastring2codonmat(cds, shorten = FALSE, frame = 1, framelist = NULL)

Arguments

cds	DNAStringSet [mandatory]
shorten	shorten all sequences to multiple of three [default: FALSE]
frame	indicates the first base of a the first codon [default: 1]
framelist	supply vector of frames for each entry [default: NULL]

Value

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

Author(s)

Kristian K Ullrich

See Also

as.alignment

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
#dnastring2codonmat(cds1.cds2.aln)
cds1.cds2.aln |> dnastring2codonmat()
## use frame 2 and shorten to circumvent multiple of three error
cds1 <- Biostrings::DNAString("-ATGCAACATTGC-")
cds2 <- Biostrings::DNAString("-ATG---CATTGC-")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
cds1.cds2.aln |> dnastring2codonmat(frame=2, shorten=TRUE)

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.