Files in scristia/CNPBayes
Bayesian mixture models for copy number polymorphisms
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/MultiBatch.R
R/MultiBatchList.R
R/MultiBatchP.R
R/RcppExports.R
R/augment.R
R/coerce-methods.R
R/data.R
R/functions.R
R/genotype_cnps.R
R/help.R
R/marginal_likelihood.R
R/methods-Hyperparameters.R
R/methods-McmcChains.R
R/methods-McmcParams.R
R/methods-MixtureModel.R
R/methods-MultiBatchModel.R
R/methods-MultiBatchPooled.R
R/methods-SingleBatchModel.R
R/methods-SingleBatchPooled.R
R/methods-SummarizedExperiment.R
R/model_initialization.R
R/plot-functions.R
R/posteriorSimulation-methods.R
R/simulate_data.R
R/zzz.R
README.Rmd
README.md
README_files/figure-gfm/downsample2-1.png
README_files/figure-gfm/posterior_summaries-1.png
README_files/figure-gfm/posteriorpredictive-1.png
README_files/figure-html/down_sample2-1.png
README_files/figure-html/downsample2-1.png
README_files/figure-html/mixtures-1.png
README_files/figure-html/posterior_predictive-1.png
README_files/figure-html/posterior_summaries-1.png
README_files/figure-html/posteriorpredictive-1.png
data-raw/cnp_data.R
data-raw/cnp_se.R
data-raw/cnv_region.R
data-raw/examples.R
data-raw/hapmap_data.R
data/MultiBatchModelExample.rda
data/MultiBatchPooledExample.rda
data/SingleBatchModelExample.rda
inst/JAGS/cnv_assoc.jag
inst/extdata/CNP_001/batched_data.rds
inst/extdata/CNP_001/mb_subsamp.rds
inst/extdata/CNP_014/mb_subsamp.rds
inst/extdata/CNP_022/mb_subsamp.rds
inst/extdata/CNP_029/mb_subsamp.rds
inst/extdata/CNP_147/mb_subsamp.rds
inst/extdata/CNP_244/mb_subsamp.rds
inst/extdata/cnp_se.rds
inst/extdata/full_001.rds
inst/extdata/mb2_001.rds
inst/extdata/sb3_001.rds
inst/extdata/snp_se.rds
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/CNPBayes.Rd
man/Hyperparameters-class.Rd
man/Hyperparameters.Rd
man/HyperparametersMultiBatch-class.Rd
man/HyperparametersMultiBatch.Rd
man/HyperparametersSingleBatch-class.Rd
man/HyperparametersSingleBatch.Rd
man/HyperparametersTrios-class.Rd
man/McmcChains-class.Rd
man/McmcParams-class.Rd
man/McmcParams.Rd
man/MixtureModel-class.Rd
man/MultiBatch-accessors.Rd
man/MultiBatch-class.Rd
man/MultiBatch.Rd
man/MultiBatchList.Rd
man/MultiBatchModel-class.Rd
man/MultiBatchModelExample.Rd
man/MultiBatchPooledExample.Rd
man/SingleBatchCopyNumber-class.Rd
man/SingleBatchModel-class.Rd
man/SingleBatchModelExample.Rd
man/bafLikelihood.Rd
man/batch-method.Rd
man/bayesFactor.Rd
man/bic-method.Rd
man/burnin-method.Rd
man/chains-method.Rd
man/cnv_models.Rd
man/consensusCNP.Rd
man/down_sample2.Rd
man/findSurrogates-MultiBatch-method.Rd
man/fit_restricted2.Rd
man/genotype_model.Rd
man/ggplot-functions.Rd
man/hemdel_model.Rd
man/homdel_model.Rd
man/homdeldup_model.Rd
man/hyperParams-method.Rd
man/id-method.Rd
man/isSimulated.Rd
man/iter-method.Rd
man/k-method.Rd
man/kolmogorov_batches.Rd
man/log_lik-method.Rd
man/map_z.Rd
man/mapping.Rd
man/marginalLik.Rd
man/marginalLikelihood-method.Rd
man/marginal_lik.Rd
man/mcmcParams-method.Rd
man/mcmcWithHomDel.Rd
man/median_summary.Rd
man/mixture_layout.Rd
man/mixture_plot.Rd
man/modelName-MixtureModel-method.Rd
man/modelName.Rd
man/mu-method.Rd
man/nStarts-method.Rd
man/names-methods.Rd
man/nu.0-method.Rd
man/numberObs-method.Rd
man/oned-method.Rd
man/orderModels.Rd
man/posteriorSimulation-method.Rd
man/probz-method.Rd
man/revertToMultiBatch.Rd
man/sigma2-method.Rd
man/sigma2.0-method.Rd
man/simulateBatchData.Rd
man/simulateData.Rd
man/subsetting-methods.Rd
man/summarize_region.Rd
man/tau2-method.Rd
man/theta-method.Rd
man/thin-method.Rd
man/upsample2.Rd
man/warmup.Rd
man/z-method.Rd
man/zfreq-method.Rd
refs.bib
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/miscfunctions.cpp
src/miscfunctions.h
src/multibatch.cpp
src/multibatch.h
src/multibatch_pooledvar.cpp
src/multibatch_pooledvar.h
src/multibatch_reduced.cpp
src/multibatch_reduced.h
src/pooledvar_reduced.cpp
src/triomodel.cpp
tests/testthat.R
tests/testthat/test_Constructors.R
tests/testthat/test_MultiBatchList.R
tests/testthat/test_cnv_pipeline.R
tests/testthat/test_deletion_pipeline.R
tests/testthat/test_duplication.R
tests/testthat/test_identify_batches.R
tests/testthat/test_log_ddirichlet.R
tests/testthat/test_mcmc_restart.R
tests/testthat/test_probz.R
tests/testthat/test_sort_component_labels.R
tests/testthat/test_tdistribution.R
vignettes/cnpbayes.Rmd
vignettes/cnpbayes.html
vignettes/cnpbayes.md
vignettes/cnpbayes_files/figure-html/SummarizedExperiment-1.png
vignettes/cnpbayes_files/figure-html/batchfig-1.png
vignettes/cnpbayes_files/figure-html/diploid-1.png
vignettes/cnpbayes_files/figure-html/mixmodelfig-1.png
vignettes/cnpbayes_files/figure-html/posterior_summaries-1.png
