getSelectionCoefficients {AnaCoDa} | R Documentation |
getSelectionCoefficients
calculates the selection coefficient of each codon in each gene.
getSelectionCoefficients(genome, parameter, samples = 100)
genome |
A genome object initialized with
|
parameter |
an object created by |
samples |
The number of samples used for the posterior estimates. |
A matrix with selection coefficients.
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) ## return estimates for selection coefficients s for each codon in each gene selection.coefficients <- getSelectionCoefficients(genome = genome, parameter = parameter, samples = 1000) ## End(Not run)