getCAIweights: Calculate the CAI codon weigths for a reference genome

Description Usage Arguments Value Examples

View source: R/genomeObject.R

Description

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

Usage

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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

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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.