findOptimalCodon {AnaCoDa} | R Documentation |
Find and return list of optimal codons
Description
findOptimalCodon
extracrs the optimal codon for each amino acid.
Usage
findOptimalCodon(csp)
Arguments
csp |
a |
Value
A named list with with optimal codons for each amino acid.
Examples
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")
genome <- initializeGenomeObject(file = genome_file)
sphi_init <- 1
numMixtures <- 1
geneAssignment <- rep(1, length(genome))
parameter <- initializeParameterObject(genome = genome, sphi = sphi_init,
num.mixtures = numMixtures,
gene.assignment = geneAssignment,
mixture.definition = "allUnique")
model <- initializeModelObject(parameter = parameter, model = "ROC")
samples <- 2500
thinning <- 50
adaptiveWidth <- 25
mcmc <- initializeMCMCObject(samples = samples, thinning = thinning,
adaptive.width=adaptiveWidth, est.expression=TRUE,
est.csp=TRUE, est.hyper=TRUE, est.mix = TRUE)
divergence.iteration <- 10
## Not run:
runMCMC(mcmc = mcmc, genome = genome, model = model,
ncores = 4, divergence.iteration = divergence.iteration)
csp_mat <- getCSPEstimates(parameter, CSP="Selection")
opt_codons <- findOptimalCodon(csp_mat)
## End(Not run)
[Package AnaCoDa version 0.1.4.4 Index]