calFst	calFst
calNeiDist	calNeiDist
ccfAUC	ccfAUC
classifyMut	classifyMut
compareCCF	compareCCF
compareJSI	compareJSI
compareTree	compareTree
fitSignatures	fitSignatures
getBinaryMatrix	getBinaryMatrix
getBinaryMatrix,phyloTree-method	getBinaryMatrix
getBootstrapValue	getBootstrapValue
getBootstrapValue,phyloTree-method	getBootstrapValue
getBranchType	getBranchType
getBranchType,phyloTree-method	getBranchType
getCCFMatrix	getCCFMatrix
getCCFMatrix,phyloTree-method	getCCFMatrix
getMafData	getMafData
getMafData,Maf-method	getMafData
getMafPatient	getMafPatient
getMafPatient,Maf-method	getMafPatient
getMafRef	getMafRef
getMafRef,Maf-method	getMafRef
getMutBranches	getMutBranches
getMutBranches,phyloTree-method	getMutBranches
getNonSyn_vc	getNonSyn_vc
getNonSyn_vc,Maf-method	getNonSyn_vc
getPhyloTree	getPhyloTree
getPhyloTreePatient	getPhyloTreePatient
getPhyloTreePatient,phyloTree-method	getPhyloTreePatient
getPhyloTreeRef	getPhyloTreeRef
getPhyloTreeRef,phyloTree-method	getPhyloTreeRef
getSampleInfo	getSampleInfo
getSampleInfo,Maf-method	getSampleInfo
getTree	getTree
getTree,phyloTree-method	getTree
getTreeMethod	getTreeMethod
getTreeMethod,phyloTree-method	getTreeMethod
Maf	Maf-class
Maf-class	Maf-class
MafList	MafList-class
MafList-class	MafList-class
mathScore	mathScore
mutHeatmap	mutHeatmap
mutTrunkBranch	mutTrunkBranch
phyloTree	phyloTree-class
phyloTree-class	phyloTree-class
phyloTreeList-class	phyloTreeList-class
plotCNA	plotCNA
plotMutProfile	plotMutProfile
plotMutSigProfile	plotMutSigProfile
plotPhyloTree	plotPhyloTree
readMaf	readMaf
readSegment	readSegment
runMesKit	runMesKit
subMaf	subMaf
testNeutral	testNeutral
triMatrix	triMatrix
vafCluster	vafCluster
