# NOT RUN {
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")
genome <- initializeGenomeObject(file = genome_file)
sphi_init <- c(1,1)
numMixtures <- 2
geneAssignment <- sample(1:2, length(genome), replace = TRUE) # random assignment to mixtures
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 codon specific parameters
csp_mat <- getCSPEstimates(parameter, CSP="Mutation")
# write the result directly to the filesystem as a csv file. No values are returned
getCSPEstimates(parameter, , filename=file.path(tempdir(), "csp_out.csv"), CSP="Mutation")
# }
# NOT RUN {
# }
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