getMixtureAssignmentEstimate {AnaCoDa} | R Documentation |
Returns mixture assignment estimates for each gene
Description
Posterior estimates for the mixture assignment of specified genes
Usage
getMixtureAssignmentEstimate(parameter, gene.index, samples)
Arguments
parameter |
on object created by |
gene.index |
a integer or vector of integers representing the gene(s) of interesst. |
samples |
number of samples for the posterior estimate |
Details
The returned vector is unnamed as gene ids are only stored in the genome
object,
but the gene.index
vector can be used to match the assignment to the genome.
Value
returns a vector with the mixture assignment of each gene corresbonding to gene.index
in the same order as the genome.
Examples
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)
# get the mixture assignment for all genes
mixAssign <- getMixtureAssignmentEstimate(parameter = parameter,
gene.index = 1:length(genome), samples = 1000)
# get the mixture assignment for a subsample
mixAssign <- getMixtureAssignmentEstimate(parameter = parameter,
gene.index = 5:100, samples = 1000)
# or
mixAssign <- getMixtureAssignmentEstimate(parameter = parameter,
gene.index = c(10, 30:50, 3, 90), samples = 1000)
## End(Not run)
[Package AnaCoDa version 0.1.4.4 Index]