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

Global functions
BatchModel Man page Source code
BatchModel-class Man page
BatchModelExample Man page
CNPBayes Man page
CNPBayes-package Man page
DensityBatchModel-class Man page
DensityModel Man page Source code
DensityModel-class Man page
Hyperparameters Man page Source code
Hyperparameters-class Man page
HyperparametersBatch Man page Source code
HyperparametersBatch-class Man page
HyperparametersMarginal Man page Source code
HyperparametersMarginal-class Man page
MarginalModel Man page Source code
MarginalModel-class Man page
MarginalModelExample Man page
McmcChains-class Man page
McmcParams Man page Source code
McmcParams-class Man page
MixtureModel-class Man page
SingleBatchPooledVar Source code
UnivariateBatchModel Source code
[,BatchModel,ANY,ANY,ANY-method Man page
[,BatchModel,ANY,ANY-method Man page
[,BatchModel,ANY-method Man page
[,BatchModel-method Man page
[,McmcChains,ANY,ANY,ANY-method Man page
[,McmcChains,ANY-method Man page
[,McmcChains-method Man page
[,McmcParams,ANY,ANY,ANY-method Man page
[,McmcParams,ANY-method Man page
[,McmcParams-method Man page
a Source code
annotateRegions Source code
argMax Source code
b Source code
batch Man page
batch,DensityModel-method Man page
batch,MixtureModel-method Man page
batchDensities Source code
batchElements Source code
batchLik Source code
batchdens Source code
betas Source code
bic Man page
bic,BatchModel-method Man page
bic,MarginalModel-method Man page
blockUpdates Source code Source code
blockUpdatesBatch Source code
blockUpdatesPooledVar Source code
burnin Man page
burnin,McmcParams-method Man page
burnin,MixtureModel-method Man page
burnin<- Man page
burnin<-,McmcParams-method Man page
burnin<-,MixtureModel-method Man page
burnin_singlebatch_pooled Source code
chains Man page
chains,MixtureModel-method Man page
chromosome Man page
clusters Man page
clusters,DensityModel-method Man page
collapseBatch Man page Source code
collapseBatch,BatchModel-method Man page
collapseBatch,SummarizedExperiment-method Man page
collapseBatch,numeric-method Man page
componentVariances Source code
computeModesBatch Source code
computeModesMarginal Source code
computeProbZ Source code
compute_loglik_batch Source code
compute_logprior Source code
compute_logprior_batch Source code
compute_means Source code
compute_means_batch Source code
compute_prec Source code
compute_prec_batch Source code
compute_vars Source code
compute_vars_batch Source code
consensusCNP Man page Source code
consensusRegion Source code
cumProbs Source code
dataMean Source code
dataPrec Source code
dataSd Source code
defineCnpRegions Source code
dens Source code
doKmeans Source code
downSampleEachBatch Man page Source code
downsample Man page Source code
ensureAllComponentsObserved Source code
eta.0 Man page
eta.0,Hyperparameters-method Man page
eta.0,MixtureModel-method Man page
extract Man page
findModes Source code
full_theta_pooled Source code
getK Source code Source code
hyperParams Man page
hyperParams,MixtureModel-method Man page
hyperParams<- Man page
hyperParams<-,MixtureModel,Hyperparameters-method Man page
hyperParams<-,MixtureModel-method Man page
imputeFromSampledData Source code
integerMatrix Source code
isOverfit Source code
iter Man page
iter,McmcParams-method Man page
iter,MixtureModel-method Man page
iter,burnin,nStarts,McmcParams-method Man page
iter<- Man page
iter<-,McmcParams-method Man page
iter<-,MixtureModel-method Man page
k Man page
k,DensityModel-method Man page
k,Hyperparameters-method Man page
k,MixtureModel-method Man page
k<- Man page
k<-,Hyperparameters-method Man page
k<-,Hyperparemeters-method Man page
k<-,MixtureModel-method Man page
labelSwitching Man page
labelSwitching,MixtureModel-method Man page
logBayesFactor Man page Source code
logLikc Source code
logPrior Man page
logPrior,McmcChains-method Man page
logPrior,MixtureModel-method Man page
log_ddirichlet_ Source code
log_lik Man page
log_lik,McmcChains-method Man page
log_lik,MixtureModel-method Man page
loglik Source code
loglik_pooled Source code
m2.0 Man page
m2.0,Hyperparameters-method Man page
m2.0,MixtureModel-method Man page
makeUnique Source code
map Man page Source code
mapCnProbability Man page Source code
mapModel Source code
marginalLikelihood Man page
marginalLikelihood,BatchModel,ANY-method Man page
marginalLikelihood,BatchModel-method Man page
marginalLikelihood,MarginalModel,ANY-method Man page
marginalLikelihood,MarginalModel-method Man page
marginalLikelihood,SingleBatchPooledVar,ANY-method Man page
marginalLikelihood,SingleBatchPooledVar-method Man page
marginalLikelihood,list,ANY-method Man page
marginalLikelihood,list-method Man page
marginal_theta Source code
marginal_theta_batch Source code
mcmcParams Man page
mcmcParams,MixtureModel-method Man page
mcmcParams<- Man page
mcmcParams<-,MixtureModel-method Man page
mcmc_batch Source code
mcmc_batch_burnin Source code
mcmc_marginal Source code
mcmc_marginal_burnin Source code
mcmc_singlebatch_pooled Source code
modelOtherModes Source code
modes Man page
modes,DensityModel-method Man page
modes,MixtureModel-method Man page
modes<- Man page
modes<-,MixtureModel-method Man page
mu Man page
mu,BatchModel-method Man page
mu,MarginalModel-method Man page
mu,McmcChains-method Man page
muMean Man page Source code
muc Man page Source code
multinomialPr_pooled Source code
multipleStarts Source code
nBatch Source code
nComp Source code
nStarts Man page
nStarts,McmcParams-method Man page
nStarts,MixtureModel-method Man page
nStarts<- Man page
nStarts<-,McmcParams-method Man page
nStarts<-,MixtureModel-method Man page
names,McmcChains-method Man page
newBatchModel Source code
newMarginalModel Source code
nitializeMcmc Source code
nitializeMcmcBatch Source code
nitializeMcmcPooledVar Source code
ntile Source code
nu.0 Man page
nu.0,McmcChains-method Man page
nu.0,MixtureModel-method Man page
nu0_pooled Source code
nu0c Source code
observed Source code
oned Man page
oned,MixtureModel-method Man page
p Man page Source code
p_mu_reduced Source code
p_mu_reduced_batch Source code
p_mu_reduced_pooled Source code
p_nu0_reduced Source code
p_nu0_reduced_batch Source code
p_nu0_reduced_pooled Source code
p_pmix_reduced Source code
p_pmix_reduced_batch Source code
p_pmix_reduced_pooled Source code
p_s20_reduced Source code
p_s20_reduced_batch Source code
p_s20_reduced_pooled Source code
p_sigma2_batch Source code
p_sigma_reduced Source code
p_sigma_reduced_batch Source code
p_sigma_reduced_pooled Source code
p_tau_reduced Source code
p_tau_reduced_batch Source code
p_tau_reduced_pooled Source code
p_theta_batch Source code
p_theta_zfixed_batch Source code
p_theta_zpermuted Source code
p_theta_zpermuted_batch Source code
param_updates Source code
parameterizeGammaByMeanSd Source code
permnK Source code
permutedz_reduced1 Source code
permutedz_reduced1_batch Source code
permutedz_reduced2 Source code
permutedz_reduced2_batch Source code
pic Man page Source code
plot Man page
plot,BatchModel,ANY-method Man page
plot,DensityBatchModel,ANY-method Man page
plot,DensityModel,ANY-method Man page
plot,DensityModel,numeric-method Man page
plot,MarginalModel,ANY-method Man page
plotBatch Source code
plotMarginal Source code
posteriorSimulation Man page Source code
posteriorSimulation,MixtureModel,ANY-method Man page
posteriorSimulation,MixtureModel,integer-method Man page
posteriorSimulation,MixtureModel,numeric-method Man page
posteriorSimulation,MixtureModel-method Man page
posteriorSimulationPooled Source code
posterior_cases Man page Source code
probz Man page
probz,MixtureModel-method Man page
qInverseTau2 Man page Source code
rMultinom Source code
reduced_mu Source code
reduced_mu_batch Source code
reduced_mu_pooled Source code
reduced_nu0 Source code
reduced_nu0_batch Source code
reduced_nu0_pooled Source code
reduced_pi Source code
reduced_pi_batch Source code
reduced_pi_pooled Source code
reduced_s20 Source code
reduced_s20_batch Source code
reduced_s20_pooled Source code
reduced_sigma Source code
reduced_sigma_batch Source code
reduced_sigma_pooled Source code
reduced_tau Source code
reduced_tau_batch Source code
reduced_tau_pooled Source code
reduced_z_theta_fixed Source code
relabeling Source code
restartAtChainIndex Source code
saveBatch Man page Source code
sigma Man page Source code
sigma.0 Source code
sigma2 Man page
sigma2,BatchModel-method Man page
sigma2,MarginalModel-method Man page
sigma2,McmcChains-method Man page
sigma2,missing-method Man page
sigma2.0 Man page
sigma2.0,McmcChains-method Man page
sigma2.0,MixtureModel-method Man page
sigma20c Source code
sigma2_0_pooled Source code
sigma2_pooled Source code
sigmac Man page Source code
simulateBatchData Man page Source code
simulateData Man page Source code
simulateProbeLevel Source code
simulateZ Source code
simulate_z_reduced1 Source code
simulate_z_reduced1_batch Source code
simulate_z_reduced2 Source code
simulate_z_reduced2_batch Source code
stageTwoLogLik Source code
stageTwoLogLikBatch Source code
stageTwoLogLik_pooled Source code
startAtTrueValues Source code
tableZ Source code
tau Man page Source code
tau.0 Source code
tau2 Man page
tau2,BatchModel-method Man page
tau2,MarginalModel-method Man page
tau2,McmcChains-method Man page
tauMean Man page Source code
tauc Man page Source code
theta Man page
theta,BatchModel-method Man page
theta,MarginalModel-method Man page
theta,McmcChains-method Man page
thin Man page
thin,McmcParams-method Man page
thin,MixtureModel-method Man page
tracePlot Man page
tracePlot,BatchModel-method Man page
uniqueBatch Source code Source code
update_mu Source code
update_multinomialPr Source code
update_multinomialPr_batch Source code
update_p Source code
update_sigma2 Source code
update_sigma20_batch Source code
update_sigma2_0 Source code
update_sigma2_batch Source code
update_tau2 Source code
update_theta_batch Source code
update_z Source code
update_z_batch Source code
useModes Source code
y Man page
y,DensityModel-method Man page
y,MixtureModel-method Man page
z Man page
z,McmcChains-method Man page
z,MixtureModel-method Man page
zFreq Man page
zFreq,McmcChains-method Man page
zFreq,MixtureModel-method Man page
z_pooled Source code
zfreq,McmcChains-method Man page
zfreq,MixtureModel-method Man page
Bioconductor-mirror/CNPBayes documentation built on May 29, 2017, 1:10 a.m.