CUB: Computes the Codon Usage Bias of DNA sequences

In vhica: Vertical and Horizontal Inheritance Consistence Analysis

Description

The function reads aligned sequences in a fasta file and estimates the codon usage bias for each sequence. Several methods exist to estimate CUB; so far, only the "Effective Number of Codons" (ENC) calculation is available.

Usage

CUB(file = NULL, sequence = NULL, method = "ENC")

Arguments

file	FASTA file in which aligned sequences are stored.
sequence	Alternatively, the result of seqinr::read.fasta.
method	The method used to compute CUB. "ENC": Effective Number of Codons, as described in Wright (1990).

Value

A named vector of CUB scores. Names correspond to sequence names in the dataset.

Author(s)

Aurelie Hua-Van and Arnaud Le Rouzic.

References

Wright, F. (1990). The 'effective number of codons' used in a gene. Gene, 87(1), 23-29.

See Also

div

Examples

	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
	CUB(seq.file)

Example output

    dgri     dvir     dmoj     dwil     dpse     dper     dana     dbip 
47.87244 40.18310 51.40403 48.91050 49.25746 48.89993 44.63742 42.75869 
    dkik     deug     dfic     dmel     dsim     dsec     dere     dyak 
44.80419 55.86458 46.33597 48.18881 43.45357 44.85876 44.13209 45.38671 
    dbia     dtak     dele     drho 
38.20318 42.14270 40.44045 42.95457 

vhica documentation built on March 2, 2020, 5:07 p.m.