AnaCoDa (version 0.1.1)

getCSPEstimates: Return Codon Specific Paramters (or write to csv) estimates as data.frame

Description

getCSPEstimates returns the codon specific parameter estimates for a given parameter and mixture or write it to a csv file.

Usage

getCSPEstimates(parameter, filename = NULL, CSP = "Mutation", mixture = 1,
  samples = 10)

Arguments

parameter

parameter an object created by initializeParameterObject.

filename

Posterior estimates will be written to file instead of returned if specified (format: csv).

CSP

which type of codon specific parameter should be returned (mutation (default) or selection)

mixture

estimates for which mixture should be returned

samples

The number of samples used for the posterior estimates.

Value

returns a data.frame with the posterior estimates of the models codon specific parameters or writes it directly to a csv file if filename is specified

Examples

# 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 {
# }