initializeModelObject function

Model Initialization

initializes the model object.

initializeModelObject(
  parameter,
  model = "ROC",
  with.phi = FALSE,
  fix.observation.noise = FALSE,
  rfp.count.column = 1
)

Arguments

• parameter: An object created with initializeParameterObject.

• model: A string containing the model to run (ROC, FONSE, or PA), has to match parameter object.

• with.phi: (ROC only) A boolean that determines whether or not to include empirical phi values (expression rates) for the calculations. Default value is FALSE

• fix.observation.noise: (ROC only) Allows fixing the noise term sepsilon in the observed expression dataset to its initial condition. This value should override the est.hyper=TRUE setting in initializeMCMCObject()

  The initial condition for the observed expression noise is set in the parameter object. Default value is FALSE.

• rfp.count.column: (PA and PANSE only) A number representing the RFP count column to use. Default value is 1.

Returns

This function returns the model object created.

Details

initializeModelObject initializes a model. The type of model is determined based on the string passed to the model argument. The Parameter object has to match the model that is initialized. E.g. to initialize a ROC model, it is required that a ROC parameter object is passed to the function.

Examples

#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 <- c(rep(1,floor(length(genome)/2)),rep(2,ceiling(length(genome)/2)))
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)