Man pages for KarchinLab/pictograph
Tools for modeling clonal evolution of a cancer
| allThreshes | defines the thresholds to be used for tree building |
| calcSubcloneProportions | Calculate proportions of subclones in each sample (assumes... |
| calcTreeScores | Calculate SCHISM fitness scores for trees |
| calculateTreeScoreMutations | Calculate SCHISM fitness scores for trees |
| collectBestKChains | Collect chains for best K of each mutation set |
| colorScheme | generate colors for each vertice |
| enumerateSpanningTreesModified | Enumerate all spanning trees using modified Gabow-Myers |
| estimateClusterAssignments | Determine most probable mutation cluster assignments by... |
| estimateICN | Determine most probable integer assignments by taking those... |
| estimateMCFs | Determine the most probable cluster MCF values by taking the... |
| estimateMultiplicity | Determine most probable mutation cluster assignments by... |
| filterEdgesBasedOnCCFs | Filter possible edges based on lineage precedence |
| generateAllTrees | Enumerate all spanning trees using modified Gabow-Myers... |
| importFiles | read input data file and store in required format |
| importMutationFileOnly | import mutation file |
| mcmcMain | run PICTograph in an automated pipeline |
| mergeSetChains | Relabel chains for all sets and merge |
| pictograph-package | pictograph |
| plotAllTrees | Plot all trees with the highest scores |
| plotChainsMCF | Plot CCF chain trace |
| plotClusterAssignmentProbVertical | Plot probabilities of mutation cluster assignments - vertical |
| plotEnsembleTree | Plot ensemble tree |
| plotMCFViolin | Plot cluster CCF posterior distributions as violin plots |
| plotSubcloneBar | Plot subclone proportions in each sample as stacked bar chart |
| plotSubclonePie | Plot pie charts for subclone proportions in each sample |
| plotTree | Plot single tree |
| prepareGraph | Create tibble of possible edges from CCF values based on... |
| runMCMCForAllBoxes | run MCMC using JAGS |
| separateMutationsBySamplePresence | sample presence for MCMC |
| writeClusterAssignmentsTable | Determine most probable mutation cluster assignments by... |
| writeClusterMCFsTable | Determine the most probable cluster MCF values by taking the... |
| writeIcnTable | Determine most probable integer copy number by taking those... |
| writeMultiplicityTable | Determine most probable multiplicity assignments by taking... |
| writeSetKTable | Make table listing possible choices of K (minimum BIC and... |
