API for Wedge-Oxford/dpclust
DPClust - An R package for subclonal reconstruction of tumours using sequencing data
| Global functions | |
|---|---|
| DPClust | Man page |
| DPClust-package | Man page |
| DensityEstimator | Source code |
| DirichletProcessClustering | Man page Source code |
| Gibbs.subclone.density.est | Source code |
| Gibbs.subclone.density.est.1d | Source code |
| Gibbs.subclone.density.est.nd | Source code |
| RunDP | Man page Source code |
| add.in.cn.as.single.snv | Man page Source code |
| add.in.cn.as.snv.cluster | Man page Source code |
| add.in.indels | Man page Source code |
| add.mutphasing | Man page Source code |
| add.muts.back.in | Source code |
| add.snv.cna.conflicts | Source code |
| add_removed_snvs | Man page Source code |
| aic | Source code |
| append.dataset | Man page Source code |
| assign_cnas_to_clusters | Man page Source code |
| bic | Source code |
| build_coassignment_prob_matrix_densities | Man page Source code |
| build_coassignment_prob_matrix_preferences | Man page Source code |
| calc.new.likelihood | Source code |
| calc_cluster_conf_intervals | Man page Source code |
| calc_cluster_order_probs | Man page Source code |
| create_pseudo_snv | Man page Source code |
| dic | Source code |
| do_uniform_sampling | Man page Source code |
| flatten_3d_to_2d | Man page Source code |
| get.conflicting.indices | Man page Source code |
| getClusterDensity | Man page Source code |
| getLocalOptima | Man page Source code |
| get_cnas_cluster_probs | Man page Source code |
| get_data_avail_for_sampling | Man page Source code |
| get_most_similar_snv | Source code |
| get_mutation_preferences | Man page Source code |
| get_snv_assignment_ccfs | Man page Source code |
| get_snv_ccf_assignmnent_density | Man page Source code |
| load.cn.data | Man page Source code |
| load.data | Man page Source code |
| load.data.inner | Source code |
| load.indel.data | Man page Source code |
| log.f.of.y | Source code |
| make_advanced_params | Man page Source code |
| make_cna_params | Man page Source code |
| make_run_params | Man page Source code |
| make_sample_params | Man page Source code |
| multiDimensionalClustering | Man page Source code |
| mutationBurdenToMutationCopyNumber | Source code |
| mutationCopyNumberToMutationBurden | Source code |
| mutation_assignment_binom | Source code |
| mutation_assignment_em | Man page Source code |
| oneDimensionalClustering | Man page Source code |
| plot1D | Man page Source code |
| plot1D_2 | Man page Source code |
| plotAssignmentTable | Man page Source code |
| plotnD | Man page Source code |
| read_gsdata_object | Man page Source code |
| reassign_1D | Source code |
| reassign_nd | Source code |
| remove_mutations | Man page Source code |
| remove_pseudo_snv_cna_clusters | Man page Source code |
| replot_1D | Source code |
| replot_nD | Source code |
| sample_mutations | Man page Source code |
| subclone.dirichlet.gibbs | Source code |
| unsample_mutations | Man page Source code |
| write.strengths.table | Source code |
| writeStandardFinalOutput | Man page Source code |
