getCAI {AnaCoDa} | R Documentation |
getCAI
returns the Codon Adaptation Index for a
genome based on a provided reference.
getCAI(referenceGenome, testGenome, default.weight = 0.5)
referenceGenome |
A genome object initialized with |
testGenome |
A genome object initialized with |
default.weight |
Default weight to use if codon is missing from referenceGenome |
Returns a named vector with the CAI for each gene
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)