API for 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
MesKit documentation built on March 28, 2021, 6 p.m.