Files in Wedge-Oxford/dpclust

DPClust - An R package for subclonal reconstruction of tumours using sequencing data

R/AssignMutations.R R/DensityEstimator.R R/DirichletProcessClustering.R R/InformationCriterions.R R/LoadData.R R/PlotDensities.R R/SampleMutations.R R/dpclust-package.R R/interconvertMutationBurdens.R R/pipeline_functions.R R/subclone_Dirichlet_Gibbs_sampler_nD_binomial.R R/util.R README.md inst/example/dpclust_pipeline.R man/DPClust.Rd man/DirichletProcessClustering.Rd man/RunDP.Rd man/add.in.cn.as.single.snv.Rd man/add.in.cn.as.snv.cluster.Rd man/add.in.indels.Rd man/add.mutphasing.Rd man/add_removed_snvs.Rd man/append.dataset.Rd man/assign_cnas_to_clusters.Rd man/build_coassignment_prob_matrix_densities.Rd man/build_coassignment_prob_matrix_preferences.Rd man/calc_cluster_conf_intervals.Rd man/calc_cluster_order_probs.Rd man/create_pseudo_snv.Rd man/do_uniform_sampling.Rd man/flatten_3d_to_2d.Rd man/get.conflicting.indices.Rd man/getClusterDensity.Rd man/getLocalOptima.Rd man/get_cnas_cluster_probs.Rd man/get_data_avail_for_sampling.Rd man/get_mutation_preferences.Rd man/get_snv_assignment_ccfs.Rd man/get_snv_ccf_assignmnent_density.Rd man/load.cn.data.Rd man/load.data.Rd man/load.indel.data.Rd man/make_advanced_params.Rd man/make_cna_params.Rd man/make_run_params.Rd man/make_sample_params.Rd man/multiDimensionalClustering.Rd man/mutation_assignment_em.Rd man/oneDimensionalClustering.Rd man/plot1D.Rd man/plot1D_2.Rd man/plotAssignmentTable.Rd man/plotnD.Rd man/read_gsdata_object.Rd man/remove_mutations.Rd man/remove_pseudo_snv_cna_clusters.Rd man/sample_mutations.Rd man/unsample_mutations.Rd man/writeStandardFinalOutput.Rd