CNPBayes: Bayesian mixture models for copy number polymorphisms

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Bayesian hierarchical mixture models for batch effects and copy number.

Author
Stephen Cristiano, Robert Scharpf, and Jacob Carey
Date of publication
None
Maintainer
Jacob Carey <jcarey15@jhu.edu>
License
Artistic-2.0
Version
1.4.0
URLs

View on Bioconductor

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.

Files in this package

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