API for CNPBayes
Bayesian mixture models for copy number polymorphisms

Global functions
BatchModel-class Man page
BatchModelExample Man page
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
DensityModel-class Man page
Hyperparameters Man page Source code
Hyperparameters-class Man page
HyperparametersBatch-class Man page
HyperparametersMarginal-class Man page
HyperparametersMultiBatch Man page Source code
HyperparametersMultiBatch-class Man page
HyperparametersSingleBatch Man page Source code
HyperparametersSingleBatch-class Man page
MB Man page Source code
MBP Man page
MarginalModel-class 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
MultiBatchCopyNumber-class Man page
MultiBatchCopyNumberPooled Man page Source code
MultiBatchCopyNumberPooled-class Man page
MultiBatchModel-class Man page
MultiBatchModel2 Man page Source code
MultiBatchModelExample Man page
MultiBatchPooled Source code
MultiBatchPooledExample Man page
SB Man page Source code
SBP Man page
SingleBatchCopyNumber Man page Source code
SingleBatchCopyNumber-class Man page
SingleBatchModel-class Man page
SingleBatchModel2 Man page Source code
SingleBatchModelExample Man page
SingleBatchPooled Man page Source code
UnivariateBatchModel Source code
[,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
aa Source code
aaab Source code
aab Source code
ab Source code
abb Source code
abbb Source code
annotateRegions Source code
argMax Source code
b Source code
bafLikelihood Man page Source code
bafs Source code
batch Man page
batch,MixtureModel-method Man page
batchElements Source code
batchLik Source code
bayesFactor Man page Source code
bb Source code
betas Source code
bic Man page
bic,MultiBatchModel-method Man page
blockUpdates Source code
blockUpdatesBatch Source code
blockUpdatesMultiBatchPooled 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
candidateModels Source code
ccmap Source code
chains Man page
chains,MixtureModel-method Man page
chains_mb Source code
chromosome Man page
chromosome,GenomicRanges-method Man page
cmap Source code
collapseBatch Man page
collapseBatch,MultiBatchModel-method Man page
collapseBatch,SummarizedExperiment-method Man page
collapseBatch,numeric-method Man page
combineBatches Source code
combine_batch Source code
combine_multibatch_pooled Source code
combine_singlebatch_pooled Source code
componentVariances Source code
computeModesBatch Source code
computeModesSBPt Source code
computeProbZ Source code
compute_heavy_means Source code
compute_heavy_means_batch Source code
compute_heavy_sums Source code
compute_heavy_sums_batch Source code
compute_loglik Source code
compute_logprior Source code
compute_marginal_lik Source code
compute_means Source code
compute_prec Source code
compute_u_sums Source code
compute_u_sums_batch Source code
compute_vars Source code
consensusCNP Man page Source code
consensusRegion Source code
copyNumber Man page
copyNumber,MultiBatchCopyNumber-method Man page
copyNumber,MultiBatchCopyNumberPooled-method Man page
cpp_burnin Source code
cpp_mcmc Source code
cumProbs Source code
d1 Source code
d2 Source code
d3 Source code
d4 Source code
d_beta Source code
dataMean Source code
dataPrec Source code
dataSd Source code
defineCnpRegions Source code
dfr Man page
dfr,Hyperparameters-method Man page
dfr,MixtureModel,numeric-method Man page
dfr,MixtureModel-method Man page
dfr<- Man page
dfr<-,Hyperparameters,numeric-method Man page
dfr<-,MixtureModel,numeric-method Man page
diagnostics Source code
dlocScale_t Source code
doKmeans Source code
downSample Man page Source code
effectiveSizeWarning Source code
empty_batch_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
findModes Source code
finiteLoglik Source code
freeParams Source code
gelmanDiag Source code
gelman_rubin Source code
genotypes Source code
getDf Source code
getK Source code Source code
ggChains Man page
ggChains,MultiBatchModel-method Man page
ggChains,MultiBatchPooled-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
ggMultiBatchChains Source code
ggMultiBatchPooledChains Source code
gg_multibatch Source code
gg_multibatch_copynumber Source code
gg_multibatch_pooled Source code
gibbs Man page Source code
gibbsMultiBatchPooled Source code
gibbsSingleBatchPooled Source code
gibbs_batch Source code
gibbs_batch_K Source code
gibbs_multibatch_pooled Source code
gibbs_singlebatch_pooled Source code
harmonizeU 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
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,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
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
log_prob_mu Source code
log_prob_nu0 Source code
log_prob_nu0p Source code
log_prob_pmix Source code
log_prob_s20 Source code
log_prob_s20p Source code
log_prob_sigma2 Source code
log_prob_sigmap Source code
log_prob_tau2 Source code
log_prob_theta Source code
log_prob_thetap Source code
loglik_multibatch_pvar 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
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
mapping,MultiBatchCopyNumberPooled,numeric-method Man page
mapping,MultiBatchCopyNumberPooled-method Man page
mapping<- Man page
mapping<-,MultiBatchCopyNumber,character-method Man page
mapping<-,MultiBatchCopyNumberPooled,character-method Man page
marginalLik Man page Source code
marginalLikelihood Man page
marginalLikelihood,MultiBatchModel,ANY-method Man page
marginalLikelihood,MultiBatchModel-method Man page
marginalLikelihood,MultiBatchPooled-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_batch Source code
marginal_theta_pooled Source code
mb_pred_data Source code
mb_predictive Source code
mclustMeans Source code
mcmcList Source code
mcmcParams Man page
mcmcParams,MixtureModel-method Man page
mcmcParams,list-method Man page
mcmcParams<- Man page
mcmcParams<-,MixtureModel-method Man page
mcmcParams<-,list-method Man page
mcmc_multibatch_pvar Source code
meltMultiBatchChains Source code
meltMultiBatchPooledChains Source code
meltSingleBatchChains Source code
meltSingleBatchPooledChains Source code
mixtureProbs Source code
mlParams Man page Source code
ml_batchmodel Source code
ml_list Source code
ml_multibatch_pooled Source code
modelName Man page Source code
modelProb Source code Source code
modes Man page
modes,MixtureModel-method Man page
modes<- Man page
modes<-,MixtureModel-method Man page
modesMultiBatchPooled Source code
mu Man page
mu,McmcChains-method Man page
mu,MixtureModel-method Man page
mu,MultiBatchModel-method Man page
muMean Man page Source code
muc Man page Source code
multibatch_figure Source code
multinomialPr_multibatch_pvar 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
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
nu0c Source code
null Source code
numberObs Man page
numberObs,MixtureModel-method Man page
observed Source code
oned Man page
oned,MixtureModel-method Man page
orderModels Man page Source code
ordered_thetas_multibatch Source code
p Man page Source code
pBAF_012 Source code Source code
pBAF_0123 Source code
pBAF_02 Source code
pBAF_12 Source code Source code
pBAF_123 Source code
pBAF_2 Source code
pBAF_23 Source code
pBAF_234 Source code
pBaf Source code
p_b Source code Source code
param_updates Source code
parameterizeGammaByMeanSd Source code
permnK Source code
pic Man page Source code
posteriorPredictive Man page Source code
posteriorSimulation Man page
posteriorSimulation,MixtureModel-method Man page
posteriorSimulation,SingleBatchModel-method Man page
posteriorSimulation,SingleBatchPooled-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
predictiveDataTable Source code
probCopyNumber Man page
probCopyNumber,MultiBatchCopyNumber-method Man page
probCopyNumber,MultiBatchCopyNumberPooled-method Man page
probTheta Source code
prob_copynumber Source code
probz Man page
probz,MixtureModel-method Man page
psParams Source code
qInverseTau2 Man page Source code
rMultinom Source code
readLocalHapmap Source code
read_hapmap Source code
reduced_mu_batch Source code
reduced_mu_pooled Source code
reduced_nu0_batch Source code
reduced_nu0_pooled Source code
reduced_pi_batch Source code
reduced_pi_pooled Source code
reduced_s20_batch Source code
reduced_sigma_batch Source code
reduced_sigma_pooled Source code
reduced_tau2_pooled Source code
reduced_tau_batch Source code
relabeling Source code
reorderMultiBatch Source code
reorderMultiBatchPooled Source code
reorderPooledVar Source code
restartAtChainIndex Source code
rlocScale_t Source code
rst 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
shapeParams Source code
sigma Man page Source code
sigma,MultiBatchCopyNumberPooled-method Man page
sigma.0 Source code
sigma2 Man page
sigma2,McmcChains-method Man page
sigma2,MixtureModel-method Man page
sigma2,MultiBatchCopyNumberPooled-method Man page
sigma2,MultiBatchPooled-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_batch Source code
sigma2_multibatch_pvar 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
smallPlates Source code
stageTwoLogLikBatch 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,McmcChains-method Man page
tau2,MixtureModel-method Man page
tau2Hyperparams Source code
tau2HyperparamsBatch Source code
tauMean Man page Source code
tauc Man page Source code
testcnp Source code
theta Man page
theta,McmcChains-method Man page
theta,MixtureModel-method Man page
thetaEffectiveSize Source code
theta_multibatch_pvar 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
upSample2 Man page Source code
updateK Source code
updateThetaBatch Source code
updateThetaPooled Source code
update_mu Source code
update_multinomialPr Source code
update_nu0 Source code
update_p Source code
update_probz Source code
update_sigma2 Source code
update_sigma20 Source code
update_tau2 Source code
update_theta Source code
update_z Source code
useModes Source code
y Man page
y,MixtureModel-method Man page
z 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
zfreq,McmcChains-method Man page
zfreq,MixtureModel-method Man page
CNPBayes documentation built on Nov. 1, 2018, 4:47 a.m.