# NOT RUN {
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)
# }
# NOT RUN {
# }
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