API for Niinleslie/MesKit
A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations
| Global functions | |
|---|---|
| Maf | Man page |
| Maf-class | Man page |
| MafList | Man page |
| MafList-class | Man page |
| byML | Source code |
| byMP | Source code |
| calChildNodeNum | Source code |
| calFst | Man page Source code |
| calJSI | Man page Source code |
| calMainTrunk | Source code |
| calNeiDist | Man page Source code |
| ccfAUC | Man page Source code |
| classifyMut | Man page Source code |
| cna2gene | Man page Source code |
| compareCCF | Man page Source code |
| compareTree | Man page Source code |
| copyNumberFilter | Source code |
| do.classify | Source code |
| drawVAFCombine | Source code |
| drawVAFCombineVline | Source code |
| fitSignatures | Man page Source code |
| getBinaryMatrix | Man page |
| getBinaryMatrix,phyloTree-method | Man page |
| getBootstrapValue | Man page |
| getBootstrapValue,phyloTree-method | Man page |
| getBranchType | Man page |
| getBranchType,phyloTree-method | Man page |
| getCCFMatrix | Man page |
| getCCFMatrix,phyloTree-method | Man page |
| getMafData | Man page |
| getMafData,Maf-method | Man page |
| getMafPatient | Man page |
| getMafPatient,Maf-method | Man page |
| getMafRef | Man page |
| getMafRef,Maf-method | Man page |
| getMutBranches | Man page |
| getMutBranches,phyloTree-method | Man page |
| getMutMatrix | Source code |
| getNodeAngle | Source code |
| getNonSyn_vc | Man page |
| getNonSyn_vc,Maf-method | Man page |
| getPhyloTree | Man page Source code |
| getPhyloTreePatient | Man page |
| getPhyloTreePatient,phyloTree-method | Man page |
| getPhyloTreeRef | Man page |
| getPhyloTreeRef,phyloTree-method | Man page |
| getPhyloTreeTsbLabel | Man page |
| getPhyloTreeTsbLabel,phyloTree-method | Man page |
| getSampleInfo | Man page |
| getSampleInfo,Maf-method | Man page |
| getSigColors | Source code |
| getTree | Man page |
| getTree,phyloTree-method | Man page |
| getTreeData | Source code |
| getTreeMethod | Man page |
| getTreeMethod,phyloTree-method | Man page |
| labelBranch | Source code |
| mathScore | Man page Source code |
| multiHits | Source code |
| mutCluster | Man page Source code |
| mutHeatmap | Man page Source code |
| mutTrunkBranch | Man page Source code |
| mutType_SP | Source code |
| mutType_SPCS | Source code |
| phyloTree | Man page |
| phyloTree-class | Man page |
| phyloTreeList-class | Man page |
| plotCNA | Man page Source code |
| plotCorr | Source code |
| plotMutProfile | Man page Source code |
| plotMutSigProfile | Man page Source code |
| plotPhyloTree | Man page Source code |
| plotPowerLaw | Source code |
| plotTree | Source code |
| readCCF | Source code |
| readGisticAllLesions | Source code |
| readGisticGene | Source code |
| readMaf | Man page Source code |
| readPhyloTree | Source code |
| readSegment | Man page Source code |
| runMesKit | Man page Source code |
| setPhyloTree | Source code |
| subMaf | Man page Source code |
| subPhyloTree | Source code |
| subTriMatrix | Source code |
| testNeutral | Man page Source code |
| treeMutationalBranches | Source code |
| triMatrix | Man page Source code |
| validCCF | Source code |
| validClinicalData | Source code |
| validMaf | Source code |
| validSeg | Source code |
