Man pages for caravagn/revolver
Repeated Evolution in Cancer (REVOLVER)

Breast.fitFit from the Yates et al. cohort of Breast cancers, with...
CRCColorectal Cancer Data by Cross et al.
CRC.cohortColorectal Cancer Data by Cross et al., in the cohort format...
jamPDFPDF jamming function
plot.rev_cohortPlot data and trees for a REVOLVER cohort.
plot.rev_cohort_fitPlot fits from a REVOLVER cohort.
plot.rev_phyloS3 method calling 'revolver_plt_tree'.
print.rev_cohortPrint a '"rev_cohort"' object
print.rev_cohort_fitPrint a REVOLVER cohort object with fits.
print.rev_phyloPrint a '"rev_phylo"' object.
revolver_analyzerWrapper for a full analysis with REVOLVER This is convenient...
revolver_check_cohortCheck basic inconsistencies in a REVOLVER cohort.
revolver_clusterCompute hierarchical clustering for a REVOLVER cohort
revolver_cohortConstruct a REVOLVER cohort object (S3 class '"rev_cohort"').
revolver_compute_CLtreesCompute/ add mutation trees to a REVOLVER cohort.
revolver_compute_phylogeniesCompute/ add CCF-based phylogenies to a REVOLVER cohort.
revolver_deletePatientsSubset the patients in the cohort to match the input list.
revolver_DETindexhelper function to calculate diversity indices
revolver_dumpStatisticsDump statistics for fit to an Excel file.
revolver_evo_distanceCompute REVOLVER's evolutionary distance h(P_i, P_j).
revolver_fitREVOLVER fit function.
revolver_infoclusteringCompute possible clusterings for standard parameters.
revolver_jackknifeComputation of fit confidence with the jackknife.
revolver_phylogenyREVOLVER constructor for an object of type "rev_phylo": a...
revolver_plt_compare_dendrogramsPlot the comparison among REVOLVER's clusters and the one...
revolver_plt_dendrogramPlot the dendrogram for REVOLVER's clusters.
revolver_plt_DET_indexPlot the DET index, via non parametric bootstrap.
revolver_plt_DET_index_driverPlot the DET index of each driver from the data (empirical).
revolver_plt_evodistancePlot REVOLVER's evolutionary distance, in a heatmap.
revolver_plt_fit_by_groupPlot model fit grouped by cluster.
revolver_plt_fit_patientPlot the tree fit for a patient.
revolver_plt_group_trajectoriesPlot the consensus model of the trajectories/
revolver_plt_itransfer_patientPlot the information transfer from a patient's fit.
revolver_plt_jackknife_coclustPlot jackknife statistics for co-clustering (heatmap).
revolver_plt_jackknife_coclust_bplotPlot jackknife statistics for co-clustering (boxplot).
revolver_plt_jackknife_edge_countsPlot jackknife statistics for the number of patients with an...
revolver_plt_jackknife_edge_prbPlot jackknife statistics for edge detection probability.
revolver_plt_patient_dataPlot a patient's data
revolver_plt_patient_treesPlot a the top-scoring trees for a patient.
revolver_plt_patient_trees_scoresPlot the scores for the trees of each patient.
revolver_plt_penalty_barplotPlot a barplot of the penalty per patient.
revolver_plt_penalty_matrixPlot a pheatmap of the penalty (patients per alterations) .
revolver_plt_rbannerplotBannerplot for REVOLVER's clusters.
revolver_plt_rclustersPlot the features of REVOLVER's clusters, in a heatmap.
revolver_plt_trajectories_patientPlot the trajectories in a patient's fit model.
revolver_plt_treePlot a phylogenetic or a mutation tree for a patient.
revolver_removeDriverRemove a driver event from a cohort.
revolver_report_fit_patientGenerate PDF report for a patient's fit
revolver_report_patientGenerate PDF report for a patient's data and trees
revolver_subsetDriversSubset the drivers in the cohort to match the input list.
stats.rev_phyloCompute statistics for a '"rev_phylo"' tree.
summary.rev_phyloSummary of a '"rev_phylo"' object.
TRACERxTRACERx mutation and CNAs Data by Jamal-Hanjani et al.,...
caravagn/revolver documentation built on May 31, 2019, 5:11 p.m.