codon_dist-methods: Calculating the codon usage difference between sequences

In Koohoko/SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

Calculating the codon usage difference between sequences

Description

We use a least squares approach to estimate the codon usage difference between DNA sequences.

Usage

codon_dist(seq, ref)

## S4 method for signature 'ANY'
codon_dist(seq, ref)

Arguments

seq	the input DNA sequnece of DNAStringSet or regioned_dna class.
ref	the reference DNA sequnece of DNAStringSet or regioned_dna class.

Details

idea inspired by "Daniel Macedo de Melo Jorge, Ryan E. Mills, Adam S. Lauring, CodonShuffle: a tool for generating and analyzing synonymously mutated sequences, Virus Evolution, Volume 1, Issue 1, March 2015, vev012, https://doi.org/10.1093/ve/vev012"

Value

vector

Examples

filepath <- system.file("extdata", "example.fasta", package = "SynMut")
rgd.seq <- input_seq(filepath)
get_cu(rgd.seq)

mut.seq <- codon_random(rgd.seq)
codon_dist(mut.seq, rgd.seq)
mut.seq2 <- codon_random(rgd.seq, keep = TRUE)
codon_dist(mut.seq2, rgd.seq)

Koohoko/SynMut documentation built on Jan. 9, 2023, 12:11 p.m.