API for CNPBayes
Bayesian mixture models for copy number polymorphisms

Global functions
BatchModel Man page Source code
BatchModel-class Man page Man page
BatchModelExample Man page
BatchModelList Man page Source code
CNPBayes Man page
CNPBayes-package Man page
CopyNumberModel Man page
CopyNumberModel,MultiBatchModel-method Man page
CopyNumberModel,MultiBatchPooled-method Man page
CopyNumberModel,SingleBatchModel-method Man page
DensityBatchModel-class Man page Man page
DensityModel Man page Man page Source code 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
HyperparametersMultiBatch Man page Source code
HyperparametersMultiBatch-class Man page
HyperparametersSingleBatch Man page Source code
HyperparametersSingleBatch-class Man page
MarginalModel-class Man page Man page
MarginalModelExample Man page
McmcChains-class Man page
McmcParams Man page Source code
McmcParams-class Man page
MixtureModel-class Man page
MultiBatchCopyNumber Man page Source code
MultiBatchCopyNumberPooled Man page Source code
MultiBatchModel Man page Source code
MultiBatchModel-class Man page
MultiBatchModel2 Man page Source code
MultiBatchModelExample Man page
MultiBatchModelList Source code
MultiBatchPooled Source code
MultiBatchPooledExample Man page
SingleBatchCopyNumber Man page Source code
SingleBatchModel Man page Source code
SingleBatchModel-class Man page
SingleBatchModel2 Man page Source code Source code
SingleBatchModelExample Man page
SingleBatchPooled Man page Source code 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
[,MultiBatchModel,ANY,ANY,ANY-method Man page
[,MultiBatchModel,ANY,ANY-method Man page
[,MultiBatchModel,ANY-method Man page
[,MultiBatchModel-method Man page
a Source code
annotateRegions Source code
argMax Source code
b Source code
batch Man page
batch,DensityModel-method Man page Man page
batch,MixtureModel-method Man page
batchDensities Source code Source code
batchElements Source code
batchLik Source code
batchdens Source code Source code
betas Source code
bic Man page
bic,BatchModel-method Man page
bic,MarginalModel-method Man page
bic,MultiBatchModel-method Man page
bic,SingleBatchModel-method Man page
blockUpdates Source code Source code
blockUpdatesBatch Source code
blockUpdatesMultiBatchPooled 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_multibatch_pvar Source code
burnin_singlebatch_pooled Source code
chains Man page
chains,MixtureModel-method Man page
chains_mb Source code
chromosome Man page
clusters Man page
collapseBatch Man page
collapseBatch,BatchModel-method Man page
collapseBatch,MultiBatchModel-method Man page
collapseBatch,SummarizedExperiment-method Man page
collapseBatch,numeric-method Man page
combineModels Source code
combinePlates Man page Source code
combinePlates,numeric-method Man page
combine_batch Source code
combine_multibatch_pooled Source code
combine_singlebatch_pooled Source code
componentVariances Source code
computeML Source code
computeModesBatch Source code
computeModesSBP Source code
computeModesSingleBatch Source code
computeProbZ Source code
compute_loglik_batch Source code
compute_logprior Source code
compute_logprior_batch Source code
compute_marginal_lik 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
copyNumber Man page
copyNumber,MultiBatchCopyNumber-method Man page
copyNumber,MultiBatchCopyNumberPooled-method Man page
copyNumber,SingleBatchCopyNumber-method Man page
cumProbs Source code
dataMean Source code
dataPrec Source code
dataSd Source code
defineCnpRegions Source code
dens Source code Source code
diagnostics Source code
dnorm_poly Source code Source code
dnorm_poly_multibatch Source code
dnorm_poly_multibatch_pooled Source code
dnorm_quantiles Source code
dnorm_singlebatch Source code
doKmeans Source code Source code
downSampleEachBatch Man page Source code
downsample Man page Source code
effectiveSizeWarning Source code
empty_batch_model Source code
empty_singlebatch_model Source code
ensureAllComponentsObserved Source code
eta.0 Man page
eta.0,Hyperparameters-method Man page
eta.0,MixtureModel-method Man page
extract Man page
failEffectiveSize Source code
failSmallPstar Source code
findModes Source code Source code
finiteLoglik Source code
full_theta_pooled Source code
gelmanDiag Source code
gelman_rubin Source code
getK Source code Source code
ggChains Man page
ggChains,MultiBatchModel-method Man page
ggChains,MultiBatchPooled-method Man page
ggChains,SingleBatchModel-method Man page
ggChains,SingleBatchPooled-method Man page
ggMixture Man page
ggMixture,MultiBatchCopyNumber-method Man page
ggMixture,MultiBatchCopyNumberPooled-method Man page
ggMixture,MultiBatchModel-method Man page
ggMixture,MultiBatchPooled-method Man page
ggMixture,SingleBatchCopyNumber-method Man page
ggMixture,SingleBatchModel-method Man page
ggMultiBatch Man page
ggMultiBatch,BatchModel-method Man page
ggMultiBatch,MultiBatchCopyNumber-method Man page
ggMultiBatch,MultiBatchModel-method Man page
ggMultiBatch,MultiBatchPooled-method Man page
ggMultiBatchChains Source code
ggMultiBatchPooledChains Source code
ggPredictive Man page Source code
ggSingleBatch Man page
ggSingleBatch,MarginalModel-method Man page
ggSingleBatch,SingleBatchCopyNumber-method Man page
ggSingleBatch,SingleBatchModel-method Man page
ggSingleBatchChains Man page Source code
ggSingleBatchPooledChains Source code
gg_multibatch Source code
gg_multibatch_copynumber Source code
gg_multibatch_pooled Source code
gg_singlebatch Source code
gg_singlebatch_copynumber Source code
gibbs Man page Source code Source code
gibbsMultiBatchPooled Source code
gibbsPooled Source code
gibbsSingleBatchPooled Source code
gibbs_K Source code
gibbs_all Man page Source code
gibbs_batch Source code
gibbs_batch_K Source code
gibbs_multibatch_pooled Source code
gibbs_pooled Man page Source code
gibbs_singlebatch_pooled Source code
hpList Man page 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
isOutlier Source code
isPooled 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 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
label_switch Man page
label_switch,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_multibatch_pvar 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
manyToOneMapping Source code
mapCnProbability Man page Source code
mapComponents Man page Source code
mapCopyNumber Man page Source code
mapModel Source code
mapParams Man page Source code
map_z Man page Source code
mapping Man page
mapping,MultiBatchCopyNumber,numeric-method Man page
mapping,MultiBatchCopyNumber-method Man page Man page
mapping,MultiBatchCopyNumberPooled,numeric-method Man page
mapping,MultiBatchCopyNumberPooled-method Man page
mapping,SingleBatchCopyNumber,numeric-method Man page
mapping,SingleBatchCopyNumber-method Man page
mapping<- Man page
mapping<-,MultiBatchCopyNumber,numeric-method Man page
mapping<-,MultiBatchCopyNumberPooled,numeric-method Man page
mapping<-,SingleBatchCopyNumber,numeric-method Man page
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,MultiBatchModel,ANY-method Man page Man page
marginalLikelihood,MultiBatchModel-method Man page
marginalLikelihood,MultiBatchPooled-method Man page
marginalLikelihood,SingleBatchModel,ANY-method Man page
marginalLikelihood,SingleBatchModel-method Man page
marginalLikelihood,SingleBatchPooled,ANY-method Man page
marginalLikelihood,SingleBatchPooled-method Man page
marginalLikelihood,list,ANY-method Man page
marginalLikelihood,list-method Man page
marginal_lik Man page
marginal_lik,MixtureModel-method Man page
marginal_lik<- Man page
marginal_lik<-,MixtureModel,numeric-method Man page
marginal_theta Source code
marginal_theta_batch Source code
mb_pred_data Source code
mb_predictive Source code
mclustMeans Source code
mcmcList Source code
mcmcMultiBatchPooled Source code
mcmcParams Man page
mcmcParams,MixtureModel-method Man page Man page
mcmcParams,list-method Man page Man page
mcmcParams<- Man page
mcmcParams<-,MixtureModel-method Man page
mcmcParams<-,list-method Man page
mcmc_batch Source code
mcmc_batch_burnin Source code
mcmc_marginal Source code
mcmc_marginal_burnin Source code
mcmc_multibatch_pvar Source code
mcmc_singlebatch_pooled Source code
meltMultiBatchChains Source code
meltMultiBatchPooledChains Source code
meltSingleBatchChains Source code
meltSingleBatchPooledChains Source code
merge_components Source code
merge_mb Source code
mlParams Man page Source code
ml_batchmodel Source code
ml_list Source code
ml_multibatch_pooled Source code
ml_pooled Source code
ml_singlebatch Source code
modelOtherModes Source code
modes Man page
modes,DensityModel-method Man page Man page
modes,MixtureModel-method Man page
modes<- Man page
modes<-,MixtureModel-method Man page
modesMultiBatchPooled Source code
mu Man page
mu,BatchModel-method Man page
mu,MarginalModel-method Man page
mu,McmcChains-method Man page
mu,MultiBatchModel-method Man page
mu,SingleBatchModel-method Man page
muMean Man page Source code
mu_multibatch_pvar_red Source code
muc Man page Source code
multiBatchDensities Man page Source code
multibatch_figure Source code
multinomialPr_multibatch_pvar Source code
multinomialPr_pooled Source code
multipleStarts Source code
multipleStarts2 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
ndices_to_merge Source code
newBatchModel Source code
newMarginalModel Source code
newMultiBatchModel Source code
newSingleBatchModel Source code
nit_batchmodel Source code
nit_batchmodel2 Source code
nit_batchmodel3 Source code
nit_kmeans Source code
nit_mclust Source code
nit_priors Source code
nit_sb1 Source code
nit_sb2 Source code
nitializeMcmc Source code
nitializeMcmcBatch Source code
nitializeMcmcPooledVar Source code
nitialize_z Source code
nitialize_z_singlebatch Source code
ntile Source code
nu.0 Man page
nu.0,McmcChains-method Man page
nu.0,MixtureModel-method Man page
nu0_multibatch_pvar Source code
nu0_multibatch_pvar_red Source code
nu0_pooled Source code
nu0c Source code
numberObs Man page
numberObs,MixtureModel-method Man page
observed Source code
oned Man page
oned,MixtureModel-method Man page
ordered_thetas_multibatch Source code
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
pi_multibatch_pvar_red Source code
pic Man page Source code
plot Man page
plot,BatchModel,ANY-method Man page Man page Man page Man page
plot,DensityBatchModel,ANY-method Man page Man page
plot,DensityModel,ANY-method Man page Man page
plot,DensityModel,numeric-method Man page Man page
plot,MarginalModel,ANY-method Man page Man page
plotBatch Source code Source code
plotMarginal Source code Source code
pnu0_multibatch_pvar_red Source code
posteriorPredictive Man page 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
posteriorSimulation,list,ANY-method Man page
posteriorSimulation,list-method Man page
posteriorSimulation2 Source code
posteriorSimulationPooled Source code
posterior_cases Man page Source code
posterior_predictive_mb Source code
posterior_predictive_mbp Source code
posterior_predictive_sb Source code
posterior_predictive_sbp Source code
probCopyNumber Man page
probCopyNumber,MultiBatchCopyNumber-method Man page
probCopyNumber,MultiBatchCopyNumberPooled-method Man page
probCopyNumber,SingleBatchCopyNumber-method Man page
prob_copynumber Source code
probz Man page
probz,MixtureModel-method Man page
ps20_multibatch_pvar_red Source code
psParams Source code
psigma_multibatch_pvar_red Source code
qInverseTau2 Man page Source code
rMultinom Source code
range_quantiles Source code
readLocalHapmap Source code
read_hapmap 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
relabel_component Source code
relabel_z Source code
relabeling Source code
remap Source code
reorderMultiBatch Source code
reorderMultiBatchPooled Source code
reorderPooledVar Source code
reorderSingleBatch Source code
reorderSingleBatchChains Source code
restartAtChainIndex Source code
s20_multibatch_pvar_red Source code
saveBatch Man page Source code
sb_pred_data Source code
sb_predictive Source code
selectByLogLik Source code
selectModels Source code
set_param_names Source code
sigma Man page Source code
sigma,MultiBatchCopyNumberPooled-method Man page
sigma.0 Source code
sigma2 Man page
sigma2,BatchModel-method Man page
sigma2,MarginalModel-method Man page
sigma2,McmcChains-method Man page
sigma2,MultiBatchCopyNumberPooled-method Man page
sigma2,MultiBatchModel-method Man page
sigma2,MultiBatchPooled-method Man page
sigma2,SingleBatchModel-method Man page
sigma2,missing-method Man page
sigma2.0 Man page
sigma2.0,McmcChains-method Man page
sigma2.0,MixtureModel-method Man page
sigma20_multibatch_pvar Source code
sigma20c Source code
sigma2_0_pooled Source code
sigma2_batch Source code
sigma2_multibatch_pvar Source code
sigma2_pooled Source code
sigma_multibatch_pvar_red Source code
sigmac Man page Source code
simulateBatchData Man page Source code
simulateData Man page Source code
simulateProbeLevel Source code
simulateThetas 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
singleBatchDensities Source code
smallPlates Source code
stageTwoLogLik Source code
stageTwoLogLikBatch Source code
stageTwoLogLik_pooled Source code
stagetwo_multibatch_pvar Source code
startAtTrueValues Source code
tableBatchZ 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
tau2,MultiBatchModel-method Man page
tau2,SingleBatchModel-method Man page
tau2Hyperparams Source code
tau2HyperparamsBatch Source code
tauMean Man page Source code
tau_multibatch_pvar_red Source code
tauc Man page Source code
testcnp Source code
theta Man page
theta,BatchModel-method Man page
theta,MarginalModel-method Man page
theta,McmcChains-method Man page
theta,MultiBatchModel-method Man page
theta,SingleBatchModel-method Man page
thetaEffectiveSize Source code
theta_multibatch_pvar Source code
theta_multibatch_pvar_red Source code
thin Man page
thin,McmcParams-method Man page
thin,MixtureModel-method Man page
thin<- Man page
thin<-,MixtureModel,numeric-method Man page
tileMedians Man page Source code
tileSummaries Man page Source code
uniqueBatch Source code Source code
upSample Man page
upSample,MixtureModel-method Man page
upSample,MultiBatchModel-method Man page
updateK Source code
update_mu Source code
update_mu_batch Source code
update_multinomialPr Source code
update_multinomialPr_batch Source code
update_p Source code
update_p_batch 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_tau2_batch 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 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_multibatch_pvar Source code
z_pooled Source code
zfreq,McmcChains-method Man page
zfreq,MixtureModel-method Man page
CNPBayes documentation built on May 2, 2018, 3:57 a.m.