initializeModelObject: Model Initialization

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

Description

initializes the model object.

Usage

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.

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.

Value

This function returns the model object created.

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)

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