CNPBayes: Bayesian mixture models for copy number polymorphisms
Version 1.6.1

Bayesian hierarchical mixture models for batch effects and copy number.

Browse man pages Browse package API and functions Browse package files

AuthorStephen Cristiano, Robert Scharpf, and Jacob Carey
Bioconductor views Bayesian CopyNumberVariation
Date of publicationNone
MaintainerJacob Carey <jcarey15@jhu.edu>
LicenseArtistic-2.0
Version1.6.1
URL https://github.com/scristia/CNPBayes
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNPBayes")

Man pages

batch-method: Retrieve batches from object.
BatchModel: Create an object for running hierarchical MCMC simulations.
BatchModel-class: An object for running MCMC simulations.
BatchModelExample: This data is a simulated example of Batch data
bic-method: Calculate BIC of a model
burnin-method: Number of burnin iterations.
chains-method: Retrieve simulated chains from model object.
chromosome: Extract character vector of sequence names
clusters-method: Accessor for extracting the kmeans clusters from a...
CNPBayes: Bayesian mixture models for copy number estimation
collapseBatch-method: Estimate batch from a collection of chemistry plates or some...
consensusCNP: Identify consensus start and stop coordinates of a copy...
DensityModel: Constructor for DensityModel class
DensityModel-class: An object to store estimated mixture model densities
downsample: Create tile labels for each observation
downSampleEachBatch: Create tile labels for each observation
eta.0-method: Retrieve the rate parameter for the tau2 distribution.
extract-methods: extract data, latent variable, and batch for given...
Hyperparameters: Create an object of class 'Hyperparameters'
HyperparametersBatch: Create an object of class 'HyperparametersBatch' for the...
HyperparametersBatch-class: An object to specify the hyperparameters of a batch effect...
Hyperparameters-class: An object to specify the hyperparameters of a model.
HyperparametersMarginal: Create an object of class 'HyperparametersMarginal' for the...
HyperparametersMarginal-class: An object to specify the hyperparameters of a marginal model.
hyperParams-method: Accessor for Hyperparameters object for a...
iter-method: Reset number of iterations.
k-method: Number of components.
labelSwitching-method: Calculate proportion of relabeling instances
logBayesFactor: Compute the log bayes factor between models.
log_lik-method: Retrieve log likelihood.
logPrior-method: Calculate log likelihood of prior for model
m2.0-method: Retrieve the shape parameter for the tau2 distribution.
map: Calculate the maximum a posteriori estimate of latent...
mapCnProbability: Probabiliistic copy number assigments.
marginalLikelihood-method: Compute the marginal likelihood of a converged model.
MarginalModel: Create an object for running marginal MCMC simulations.
MarginalModel-class: The 'MarginalModel' class
MarginalModelExample: This data is a simulated example of Marginal data
McmcChains-class: An object to hold estimated paraeters.
McmcParams: Create an object of class 'McmcParams' to specify iterations,...
McmcParams-class: An object to specify MCMC options for a later simulation
mcmcParams-method: Retrieve MCMC parameters from model.
MixtureModel-class: An object for running MCMC simulations.
modes-method: Retrieve the modes from a model.
muc: Retrieve overall mean at each iteration of the MCMC.
muMean: Retrieve overall mean averaged across MCMC simulations.
mu-method: Retrieve overall mean
names-methods: Retrieve the names of the parameters estimated in the MCMC...
nStarts-method: Number of MCMC chains.
nu.0-method: Retrieve the shape parameter for the sigma.2 distribution.
oned-method: Retrieve data.
p: Retrieve mixture proportions.
pic: Retrieve mixture proportions at each iteration of the MCMC.
plot: Plot the densities estimated from a mixture model for a copy...
posterior_cases: Calculate posterior proportion of cases by component
posteriorSimulation-method: Run the MCMC simulation.
probz-method: Retrieve the probability of latent variable membership by...
qInverseTau2: Quantiles, shape, and rate of the prior for the inverse of...
saveBatch: Save se data
sigma: Retrieve standard deviations of each component/batch mean.
sigma2.0-method: Retrieve the rate parameter for the sigma.2 distribution.
sigma2-method: Retrieve the variances of each component and batch...
sigmac: Retrieve standard deviation of each component/batch mean at...
simulateBatchData: Create simulated batch data for testing.
simulateData: Create simulated data for testing.
tau: Retrieve overall standard deviation.
tau2-method: Accessor for the tau2 parameter in the hierarchical mixture...
tauc: Retrieve overall standard deviation at each iteration of the...
tauMean: Retrieve overall standard deviation averaged across MCMC...
theta-method: Accessor for the theta parameter in the hierarchical mixture...
thin-method: Number of thinning intervals.
tracePlot-method: Create a trace plot of a parameter estimated by MCMC.
y-method: Retrieve data.
zfreq-method: Calculates a frequency table of latent variable assigments by...
z-method: Retrieve latent variable assignments.

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

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/RcppExports.R
R/data.R
R/functions.R
R/help.R
R/marginal_likelihood.R
R/methods-BatchModel.R
R/methods-DensityModel.R
R/methods-Hyperparameters.R
R/methods-MarginalModel.R
R/methods-McmcChains.R
R/methods-McmcParams.R
R/methods-MixtureModel.R
R/methods-SummarizedExperiment.R
R/model_initialization.R
R/relabeling.R
R/simulate_data.R
R/visualization.R
README.md
build
build/vignette.rds
data
data/BatchModelExample.RData
data/MarginalModelExample.RData
inst
inst/doc
inst/doc/Convergence.R
inst/doc/Convergence.Rmd
inst/doc/Convergence.pdf
inst/doc/FindCNPs.R
inst/doc/FindCNPs.Rmd
inst/doc/FindCNPs.pdf
inst/doc/Implementation.R
inst/doc/Implementation.Rmd
inst/doc/Implementation.pdf
inst/doc/Overview.R
inst/doc/Overview.Rmd
inst/doc/Overview.pdf
inst/extdata
inst/extdata/baf.rds
inst/extdata/grl_deletions.rds
inst/extdata/hgTables.txt
inst/extdata/simulated_se.rds
inst/scripts
inst/scripts/run_simulation.R
inst/scripts/run_simulation_hard.R
inst/scripts/simulate-probes.R
inst/scripts/simulations.r
inst/scripts/summarizedata.r
inst/simulate_cnvs.org
inst/skewnormal_mix.cpp
man
man/BatchModel-class.Rd
man/BatchModel.Rd
man/BatchModelExample.Rd
man/CNPBayes.Rd
man/DensityModel-class.Rd
man/DensityModel.Rd
man/Hyperparameters-class.Rd
man/Hyperparameters.Rd
man/HyperparametersBatch-class.Rd
man/HyperparametersBatch.Rd
man/HyperparametersMarginal-class.Rd
man/HyperparametersMarginal.Rd
man/MarginalModel-class.Rd
man/MarginalModel.Rd
man/MarginalModelExample.Rd
man/McmcChains-class.Rd
man/McmcParams-class.Rd
man/McmcParams.Rd
man/MixtureModel-class.Rd
man/batch-method.Rd
man/bic-method.Rd
man/burnin-method.Rd
man/chains-method.Rd
man/chromosome.Rd
man/clusters-method.Rd
man/collapseBatch-method.Rd
man/consensusCNP.Rd
man/downSampleEachBatch.Rd
man/downsample.Rd
man/eta.0-method.Rd
man/extract-methods.Rd
man/hyperParams-method.Rd
man/iter-method.Rd
man/k-method.Rd
man/labelSwitching-method.Rd
man/logBayesFactor.Rd
man/logPrior-method.Rd
man/log_lik-method.Rd
man/m2.0-method.Rd
man/map.Rd
man/mapCnProbability.Rd
man/marginalLikelihood-method.Rd
man/mcmcParams-method.Rd
man/modes-method.Rd
man/mu-method.Rd
man/muMean.Rd
man/muc.Rd
man/nStarts-method.Rd
man/names-methods.Rd
man/nu.0-method.Rd
man/oned-method.Rd
man/p.Rd
man/pic.Rd
man/plot.Rd
man/posteriorSimulation-method.Rd
man/posterior_cases.Rd
man/probz-method.Rd
man/qInverseTau2.Rd
man/saveBatch.Rd
man/sigma.Rd
man/sigma2-method.Rd
man/sigma2.0-method.Rd
man/sigmac.Rd
man/simulateBatchData.Rd
man/simulateData.Rd
man/tau.Rd
man/tau2-method.Rd
man/tauMean.Rd
man/tauc.Rd
man/theta-method.Rd
man/thin-method.Rd
man/tracePlot-method.Rd
man/y-method.Rd
man/z-method.Rd
man/zfreq-method.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/miscfunctions.cpp
src/miscfunctions.h
src/reduced_pooledvariance.cpp
src/singlebatch_pooledvar.cpp
src/singlebatch_pooledvar.h
src/update.cpp
src/update.h
src/updates_batch.cpp
src/updates_batch.h
src/updates_marginal.cpp
src/updates_marginal.h
src/updates_reduced_batch.cpp
src/updates_reduced_batch.h
src/updates_reduced_marginal.cpp
src/updates_reduced_marginal.h
tests
tests/testthat
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/test_Constructors.R
tests/testthat/test_batch.R
tests/testthat/test_cnProbability.R
tests/testthat/test_cnpRegions.R
tests/testthat/test_compute_means.R
tests/testthat/test_consensusCNPs.R
tests/testthat/test_currentExtData.R
tests/testthat/test_external.R
tests/testthat/test_log_ddirichlet.R
tests/testthat/test_loglik.R
tests/testthat/test_marginal.R
tests/testthat/test_marginal_likelihood.R
tests/testthat/test_mcmc_restart.R
tests/testthat/test_plotting.R
tests/testthat/test_probz.R
tests/testthat/test_qInverseTau2.R
tests/testthat/test_relabel.R
tests/testthat/test_selection.R
tests/testthat/test_sigma2_pooled.R
tests/testthat/test_simulation.R
tests/testthat/test_summmarizedExperiment.R
tests/testthat/test_update_p.R
vignettes
vignettes/Convergence.Rmd
vignettes/FindCNPs.Rmd
vignettes/Implementation.Rmd
vignettes/Overview.Rmd
vignettes/references.bib
CNPBayes documentation built on May 20, 2017, 10:33 p.m.