Man pages for Bioconductor-mirror/CNPBayes
Bayesian mixture models for copy number polymorphisms

batch-methodRetrieve batches from object.
BatchModelCreate an object for running hierarchical MCMC simulations.
BatchModel-classAn object for running MCMC simulations.
BatchModelExampleThis data is a simulated example of Batch data
bic-methodCalculate BIC of a model
burnin-methodNumber of burnin iterations.
chains-methodRetrieve simulated chains from model object.
chromosomeExtract character vector of sequence names
clusters-methodAccessor for extracting the kmeans clusters from a...
CNPBayesBayesian mixture models for copy number estimation
collapseBatch-methodEstimate batch from a collection of chemistry plates or some...
consensusCNPIdentify consensus start and stop coordinates of a copy...
DensityModelConstructor for DensityModel class
DensityModel-classAn object to store estimated mixture model densities
downsampleCreate tile labels for each observation
downSampleEachBatchCreate tile labels for each observation
eta.0-methodRetrieve the rate parameter for the tau2 distribution.
extract-methodsextract data, latent variable, and batch for given...
HyperparametersCreate an object of class 'Hyperparameters'
HyperparametersBatchCreate an object of class 'HyperparametersBatch' for the...
HyperparametersBatch-classAn object to specify the hyperparameters of a batch effect...
Hyperparameters-classAn object to specify the hyperparameters of a model.
HyperparametersMarginalCreate an object of class 'HyperparametersMarginal' for the...
HyperparametersMarginal-classAn object to specify the hyperparameters of a marginal model.
hyperParams-methodAccessor for Hyperparameters object for a...
iter-methodReset number of iterations.
k-methodNumber of components.
labelSwitching-methodCalculate proportion of relabeling instances
logBayesFactorCompute the log bayes factor between models.
log_lik-methodRetrieve log likelihood.
logPrior-methodCalculate log likelihood of prior for model
m2.0-methodRetrieve the shape parameter for the tau2 distribution.
mapCalculate the maximum a posteriori estimate of latent...
mapCnProbabilityProbabiliistic copy number assigments.
marginalLikelihood-methodCompute the marginal likelihood of a converged model.
MarginalModelCreate an object for running marginal MCMC simulations.
MarginalModel-classThe 'MarginalModel' class
MarginalModelExampleThis data is a simulated example of Marginal data
McmcChains-classAn object to hold estimated paraeters.
McmcParamsCreate an object of class 'McmcParams' to specify iterations,...
McmcParams-classAn object to specify MCMC options for a later simulation
mcmcParams-methodRetrieve MCMC parameters from model.
MixtureModel-classAn object for running MCMC simulations.
modes-methodRetrieve the modes from a model.
mucRetrieve overall mean at each iteration of the MCMC.
muMeanRetrieve overall mean averaged across MCMC simulations.
mu-methodRetrieve overall mean
names-methodsRetrieve the names of the parameters estimated in the MCMC...
nStarts-methodNumber of MCMC chains.
nu.0-methodRetrieve the shape parameter for the sigma.2 distribution.
oned-methodRetrieve data.
pRetrieve mixture proportions.
picRetrieve mixture proportions at each iteration of the MCMC.
plotPlot the densities estimated from a mixture model for a copy...
posterior_casesCalculate posterior proportion of cases by component
posteriorSimulation-methodRun the MCMC simulation.
probz-methodRetrieve the probability of latent variable membership by...
qInverseTau2Quantiles, shape, and rate of the prior for the inverse of...
saveBatchSave se data
sigmaRetrieve standard deviations of each component/batch mean.
sigma2.0-methodRetrieve the rate parameter for the sigma.2 distribution.
sigma2-methodRetrieve the variances of each component and batch...
sigmacRetrieve standard deviation of each component/batch mean at...
simulateBatchDataCreate simulated batch data for testing.
simulateDataCreate simulated data for testing.
tauRetrieve overall standard deviation.
tau2-methodAccessor for the tau2 parameter in the hierarchical mixture...
taucRetrieve overall standard deviation at each iteration of the...
tauMeanRetrieve overall standard deviation averaged across MCMC...
theta-methodAccessor for the theta parameter in the hierarchical mixture...
thin-methodNumber of thinning intervals.
tracePlot-methodCreate a trace plot of a parameter estimated by MCMC.
y-methodRetrieve data.
zfreq-methodCalculates a frequency table of latent variable assigments by...
z-methodRetrieve latent variable assignments.
Bioconductor-mirror/CNPBayes documentation built on May 29, 2017, 1:10 a.m.