AnaCoDa (version 0.1.1)

getCAI: Calculate the Codon Adaptation Index

Description

getCAI returns the Codon Adaptation Index for a genome based on a provided reference.

Usage

getCAI(referenceGenome, testGenome)

Arguments

referenceGenome

A genome object initialized with initializeGenomeObject. Serves as reference set to calculate the necessary codon weights.

testGenome

A genome object initialized with initializeGenomeObject. The genome for which the CAI is supposed to be calculated

Value

Returns a named vector with the CAI for each gene

Examples

# NOT RUN {
genome_file1 <- system.file("extdata", "more_genes.fasta", package = "AnaCoDa")
genome_file2 <- system.file("extdata", "genome.fasta", package = "AnaCoDa")

## reading genome
referenceGenome <- initializeGenomeObject(file = genome_file1)
testGenome <- initializeGenomeObject(file = genome_file2)

cai <- getCAI(referenceGenome, testGenome)

# }

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