CNPBayes: Bayesian mixture models for copy number polymorphisms

Bayesian hierarchical mixture models for batch effects and copy number.

AuthorStephen Cristiano, Robert Scharpf, and Jacob Carey
Date of publicationNone
MaintainerJacob Carey <jcarey15@jhu.edu>
LicenseArtistic-2.0
Version1.4.0
https://github.com/scristia/CNPBayes

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

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