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 |

https://github.com/scristia/CNPBayes |

**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.

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

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