getSelectionCoefficients {AnaCoDa} | R Documentation |
Calculate Selection coefficients
Description
getSelectionCoefficients
calculates the selection coefficient of each codon in each gene.
Usage
getSelectionCoefficients(genome, parameter, samples = 100)
Arguments
genome |
A genome object initialized with
|
parameter |
an object created by |
samples |
The number of samples used for the posterior estimates. |
Value
A matrix with selection coefficients.
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)
## return estimates for selection coefficients s for each codon in each gene
selection.coefficients <- getSelectionCoefficients(genome = genome,
parameter = parameter, samples = 1000)
## End(Not run)
[Package AnaCoDa version 0.1.4.4 Index]