# NOT RUN {
#initializing a model object
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")
expression_file <- system.file("extdata", "expression.csv", package = "AnaCoDa")
genome <- initializeGenomeObject(file = genome_file,
observed.expression.file = expression_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")
# initializing a model object assuming we have observed expression (phi)
# values stored in the genome object.
initializeModelObject(parameter = parameter, model = "ROC", with.phi = TRUE)
# initializing a model object ignoring observed expression (phi)
# values stored in the genome object.
initializeModelObject(parameter = parameter, model = "ROC", with.phi = FALSE)
# }
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