getCAIweights function

Calculate the CAI codon weigths for a reference genome

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

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

Returns

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)