getSelectionCoefficients: Calculate Selection coefficients

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

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 initializeGenomeObject to add observed expression data.
parameter	an object created by initializeParameterObject.
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)

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.