getCAIweights: Calculate the CAI codon weigths for a reference genome

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

getCAIweights returns the weights for the Codon Adaptation Index based on a reference genome.

Usage

getCAIweights(referenceGenome, default.weight = 0.5)

Arguments

referenceGenome	A genome object initialized with initializeGenomeObject.
default.weight	Set default weight for any codon not observed in the reference genome

Value

Returns a named vector with the CAI weights for each codon

Examples

genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")

## reading genome
referenceGenome <- initializeGenomeObject(file = genome_file)

wi <- getCAIweights(referenceGenome)

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.