CUB {vhica} | R Documentation |
Computes the Codon Usage Bias of DNA sequences
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
Examples
seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
CUB(seq.file)
[Package vhica version 0.2.8 Index]