Maf-class               Maf class
MafList-class           MafList class
calFst                  calFst
calJSI                  compareJSI
calNeiDist              calNeiDist
ccfAUC                  ccfAUC
classifyMut             classifyMut
cna2gene                cna2gene
compareCCF              compareCCF
compareTree             compareTree
fitSignatures           fitSignatures
getBinaryMatrix         getBinaryMatrix
getBootstrapValue       getBootstrapValue
getBranchType           getBranchType
getCCFMatrix            getCCFMatrix
getMafData              getMafData
getMafPatient           getMafPatient
getMafRef               getMafRef
getMutBranches          getMutBranches
getNonSyn_vc            getNonSyn_vc
getPhyloTree            getPhyloTree
getPhyloTreePatient     getPhyloTreePatient
getPhyloTreeRef         getPhyloTreeRef
getPhyloTreeTsbLabel    getPhyloTreeRef
getSampleInfo           getSampleInfo
getTree                 getTree
getTreeMethod           getTreeMethod
mathScore               mathScore
mutCluster              mutCluster
mutHeatmap              mutHeatmap
mutTrunkBranch          mutTrunkBranch
phyloTree-class         phyloTree class
phyloTreeList-class     phyloTreeList class
plotCNA                 plotCNA
plotMutProfile          plotMutProfile
plotMutSigProfile       plotMutSigProfile
plotPhyloTree           plotPhyloTree
readMaf                 readMaf
readSegment             readSegment
runMesKit               Run the default MesKit app for analysis locally
subMaf                  Subset Maf object
testNeutral             testNeutral
triMatrix               triMatrix
