Files in CNPBayes
Bayesian mixture models for copy number polymorphisms

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 31, 2017, 2:57 p.m.