get_freq-methods: Get codon usage frequency of synonymous codons

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

Get codon usage frequency of synonymous codons

Description

Access the synonymous codon usage frequency

Usage

get_freq(object, numcode = 1, ...)

## S4 method for signature 'regioned_dna'
get_freq(object, numcode)

## S4 method for signature 'DNAStringSet'
get_freq(object, numcode)

## S4 method for signature 'matrix'
get_freq(object, numcode)

## S4 method for signature 'vector'
get_freq(object, numcode)

Arguments

object	regioned_dna / DNAStringSet / codon usage matrix (vector)
numcode	The ncbi genetic code number for translation. Default value: 1. Details please refer to ?seqinr::translate ("https://rdrr.io/cran/seqinr/man/translate.html").
...	...

Value

matrix

See Also

input_seq, get_region, get_cu, get_du, get_rscu

Examples

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

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