Man pages for caravagn/revolver
REVOLVER - Repeated Evolution in Cancer
| CCF | Extract all CCF or binary data for a patient. |
| CCF_clusters | Extract all clusters in the data of a patient. |
| CCF_parser | Parser function for the required 'CCF' input field. |
| Clonal_cluster | Extract the clonal cluster id for a patient. |
| Cluster | Get REVOLVER clusters information for this cohort |
| compute_clone_trees | Compute CCF-based clone trees for a patient (phylogenies). |
| compute_mutation_trees | Compute binary mutation trees for a patient (phylogenies). |
| Data | Extract all data for a patient. |
| DET_index | Compute the index of Divergent Evolutionary Trajectories. |
| distinct_palette_few | Palette of few distinct colours. |
| distinct_palette_many | Palette of 'n' distinct colours. |
| Drivers | Extract driver data for a patient. |
| get_features | Return summary features for the cohort. |
| gradient_palette | Gradient palette. |
| input_custom_trees | Add a custom set of trees for a patient. |
| ITransfer | Extract the information transfer available for a patient. |
| Jackknife_cluster_stability | Get jackknifed cluster stability. |
| Jackknife_patient_coclustering | Get jackknifed patient co-clustering probability. |
| Jackknife_trajectories_stability | Get jackknifed trajectories stability. |
| Phylo | Extract the trees available for a patient. |
| plot_clusters | Plot the heatmaps of REVOLVER"s clusters. |
| plot_dendrogram | Plot the dendrogram of REVOLVER"s clusters. |
| plot_DET_index | Plot the index of Divergent Evolutionary Trajectories. |
| plot_drivers_clonality | Plot the clonality status of cohort driver events. |
| plot_drivers_graph | Plot graph-alike summary statistics for the cohort drivers. |
| plot_drivers_occurrence | Plot the occurrence of drivers across the cohort. |
| plot_jackknife_cluster_stability | Plot the patients' jackknife cluster staability |
| plot_jackknife_coclustering | Plot the patients' jackknife co-clustering probability |
| plot_jackknife_trajectories_stability | Plot the patients' jackknife trajectory frequencies. |
| plot_patient_CCF_histogram | Plot the data histogram for a patient. |
| plot_patient_data | Plot the data for a patient. |
| plot_patient_mutation_burden | Plot the mutation burden for a patient. |
| plot_patient_oncoprint | Plot the oncoprint for a patient. |
| plot_patient_trees | Plot REVOLVER trees for a patient. |
| plot_patient_trees_scores | Plot the scores for a patient's trees. |
| plot_penalty | Plot the fit penalty. |
| plot.rev_cohort | Summary scatterplot of a cohort. |
| plot.rev_cohort_fit | Summary scatterplot of a cohort's fits. |
| plot_trajectories_per_cluster | Plot the number of observed trajectories in each cluster. |
| print.rev_cohort | Summary print of a cohort. |
| print.rev_cohort_fit | Summary print of a cohort with fits. |
| remove_drivers | Remove a list of driver events from the cohort. |
| remove_patients | Remove patients from the cohort. |
| revolver_check_cohort | Check basic inconsistencies in a REVOLVER cohort. |
| revolver_cluster | Compute hierarchical clustering for a REVOLVER cohort. |
| revolver_cohort | Construct a REVOLVER cohort. |
| revolver_fit | Fit a REVOLVER model. |
| revolver_jackknife | Compute clusters stability via the jackknife. |
| Samples | Extract all samples ids for a patient. |
| Stats | Summary statistics for the cohort's patients. |
| Stats_cohort | Synonim for function 'Stats'. |
| Stats_drivers | Summary statistics for the cohort's driver events. |
| Stats_fits | Summary statistics for the cohort's fits. |
| Stats_trees | Summary statistics for the cohort's trees. |
| Subclonal | Extract subclonal data for a patient. |
| Truncal | Extract clonal (i.e., truncal) data for a patient. |
