getCSPEstimates {AnaCoDa} | R Documentation |
getCSPEstimates
returns the codon specific
parameter estimates for a given parameter and mixture or write it to a csv file.
getCSPEstimates(parameter, filename = NULL, mixture = 1, samples = 10, relative.to.optimal.codon = T, report.original.ref = T)
parameter |
parameter an object created by |
filename |
Posterior estimates will be written to file (format: csv). Filename will be in the format <parameter_name>_<filename>.csv. |
mixture |
estimates for which mixture should be returned |
samples |
The number of samples used for the posterior estimates. |
relative.to.optimal.codon |
Boolean determining if parameters should be relative to the preferred codon or the alphabetically last codon (Default=TRUE). Only applies to ROC and FONSE models |
report.original.ref |
Include the original reference codon (Default = TRUE). Note this is only included for the purposes of simulations, which expect the input parameter file to be in a specific format. Later version of AnaCoDa will remove this. |
returns a list data.frame with the posterior estimates of the models
codon specific parameters or writes it directly to a csv file if filename
is specified
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa") genome <- initializeGenomeObject(file = genome_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") 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) # write the result directly to the filesystem as a csv file. No values are returned getCSPEstimates(parameter, filename=file.path(tempdir(), "test.csv")) ## End(Not run)