Files in CNPBayes
Bayesian mixture models for copy number polymorphisms

README.md
NAMESPACE
DESCRIPTION
src/singlebatch.cpp
src/multibatch.h
src/singlebatch.h
src/update.h
src/singlebatch_pooledvar.cpp
src/multibatch_pooledvar.cpp
src/multibatch_pooledvar_reduced.cpp
src/singlebatch_reduced.cpp
src/multibatch_reduced.h
src/multibatch_reduced.cpp
src/Makevars
src/multibatch.cpp
src/singlebatch_pooledvar.h
src/Makevars.win
src/multibatch_pooledvar.h
src/miscfunctions.cpp
src/RcppExports.cpp
src/singlebatch_pooledvar_reduced.cpp
src/singlebatch_reduced.h
src/update.cpp
src/miscfunctions.h
inst/skewnormal_mix.cpp
inst/simulate_cnvs.org
inst/extdata/mckean_data.rds
inst/extdata/hgTables.txt
inst/extdata/baf.rds
inst/extdata/targeted_seq.txt
inst/extdata/grl_deletions.rds
inst/extdata/expr_meth_cn_model.rds
inst/extdata/simulated_se.rds
inst/extdata/DeletionModelExample.rds
inst/doc/Implementation.pdf inst/doc/FindCNPs.pdf inst/doc/Overview.pdf inst/doc/Convergence.R inst/doc/Convergence.Rmd inst/doc/Overview.R inst/doc/FindCNPs.R inst/doc/Convergence.pdf inst/doc/Overview.Rmd inst/doc/Implementation.R inst/doc/FindCNPs.Rmd inst/doc/Implementation.Rmd inst/scripts/summarizedata.r inst/scripts/simulations.r inst/scripts/run_simulation.R inst/scripts/simulate-probes.R inst/scripts/run_simulation_hard.R R/methods-MixtureModel.R R/methods-McmcParams.R R/simulate_data.R R/AllGenerics.R R/marginal_likelihood.R R/help.R R/methods-Hyperparameters.R R/copynumber-models.R R/RcppExports.R R/methods-McmcChains.R R/relabeling.R R/functions.R R/methods-MultiBatchModel.R R/coerce-methods.R R/methods-SingleBatchModel.R R/plot-functions.R R/posteriorSimulation-methods.R R/methods-SingleBatchPooled.R R/methods-MultiBatchPooled.R R/data.R R/diagnostics.R R/model_initialization.R R/methods-SummarizedExperiment.R R/deprecated_functions.R R/AllClasses.R R/Deprecated-classes.R
build/vignette.rds
tests/testthat.R tests/testthat/test_simulation.R tests/testthat/test_loglik.R tests/testthat/test_singlebatch.R tests/testthat/test_selection.R tests/testthat/test_cnpRegions.R tests/testthat/test_currentExtData.R tests/testthat/test_log_ddirichlet.R tests/testthat/test_starting_values.R tests/testthat/test_SingleBatchPooled.R tests/testthat/test_qInverseTau2.R tests/testthat/test_MultiBatchPooled.R tests/testthat/test_mcmc_restart.R tests/testthat/test_local.R tests/testthat/test_update_p.R tests/testthat/test_posterior_predictive.R tests/testthat/test_downsample.R tests/testthat/test_copynumber-models.R tests/testthat/test_external.R tests/testthat/test_targetedseq.R tests/testthat/test_multibatch.R tests/testthat/test_probz.R tests/testthat/test_Constructors.R tests/testthat/test_ggfuns.R tests/testthat/test_sort_component_labels.R tests/testthat/test_tileMedians.R tests/testthat/test_marginal_likelihood.R vignettes/Implementation.Rmd vignettes/FindCNPs.Rmd
vignettes/references.bib
vignettes/Overview.Rmd vignettes/Convergence.Rmd
data/MarginalModelExample.RData
data/BatchModelExample.RData
data/SingleBatchModelExample.rda
data/MultiBatchPooledExample.rda
data/MultiBatchModelExample.rda
man/simulateData.Rd man/consensusCNP.Rd man/Deprecated-classes.Rd man/SingleBatchModelExample.Rd man/HyperparametersMultiBatch.Rd man/theta-method.Rd man/MultiBatchModelExample.Rd man/posterior_cases.Rd man/posteriorSimulation-method.Rd man/posteriorPredictive.Rd man/chains-method.Rd man/ggplot-functions.Rd man/chromosome.Rd man/mapCnProbability.Rd man/muc.Rd man/Deprecated-functions.Rd man/sigma.Rd man/m2.0-method.Rd man/HyperparametersSingleBatch-class.Rd man/BatchModelExample.Rd man/combinePlates-method.Rd man/mapComponents.Rd man/pic.Rd man/mu-method.Rd man/probz-method.Rd man/thin-method.Rd man/iter-method.Rd man/qInverseTau2.Rd man/MultiBatchModel2.Rd man/copyNumber.Rd man/map_z.Rd man/numberObs-method.Rd man/saveBatch.Rd man/MultiBatchPooledExample.Rd man/McmcParams-class.Rd man/HyperparametersMarginal-class.Rd man/SingleBatchModel2.Rd man/extract-methods.Rd man/modes-method.Rd man/HyperparametersBatch-class.Rd man/zfreq-method.Rd man/eta.0-method.Rd man/SingleBatchModel-class.Rd man/label_switch.Rd man/MultiBatchModel-class.Rd man/k-method.Rd man/tau.Rd man/gibbs_all.Rd man/Hyperparameters-class.Rd man/muMean.Rd man/MarginalModelExample.Rd man/McmcChains-class.Rd man/names-methods.Rd man/MixtureModel-class.Rd man/McmcParams.Rd man/tauMean.Rd man/oned-method.Rd man/Hyperparameters.Rd man/collapseBatch-method.Rd man/burnin-method.Rd man/tauc.Rd man/gibbs.Rd man/mapping.Rd man/tau2-method.Rd man/bic-method.Rd man/mapParams.Rd man/sigma2.0-method.Rd man/nu.0-method.Rd man/p.Rd man/marginalLikelihood-method.Rd man/nStarts-method.Rd man/logPrior-method.Rd man/hyperParams-method.Rd man/mcmcParams-method.Rd man/mlParams.Rd man/sigma2-method.Rd man/marginal_lik.Rd man/HyperparametersMultiBatch-class.Rd man/batch-method.Rd man/probCopyNumber.Rd man/ggPredictive.Rd man/CNPBayes.Rd man/z-method.Rd man/HyperparametersSingleBatch.Rd man/CopyNumber-methods.Rd man/tile-functions.Rd man/logBayesFactor.Rd man/y-method.Rd man/sigmac.Rd man/gibbs_pooled.Rd man/log_lik-method.Rd man/simulateBatchData.Rd
CNPBayes documentation built on Nov. 17, 2017, 8:27 a.m.