A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations


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Documentation for package ‘MesKit’ version 0.99.16

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calFst calFst
calNeiDist calNeiDist
ccfAUC ccfAUC
classifyMut classifyMut
compareCCF compareCCF
compareJSI compareJSI
compareTree compareTree
fitSignatures fitSignatures
getBinaryMatrix getBinaryMatrix
getBinaryMatrix-method getBinaryMatrix
getBootstrapValue getBootstrapValue
getBootstrapValue-method getBootstrapValue
getBranchType getBranchType
getBranchType-method getBranchType
getCCFMatrix getCCFMatrix
getCCFMatrix-method getCCFMatrix
getMafData getMafData
getMafData-method getMafData
getMafPatient getMafPatient
getMafPatient-method getMafPatient
getMafRef getMafRef
getMafRef-method getMafRef
getMutBranches getMutBranches
getMutBranches-method getMutBranches
getNonSyn_vc getNonSyn_vc
getNonSyn_vc-method getNonSyn_vc
getPhyloTree getPhyloTree
getPhyloTreePatient getPhyloTreePatient
getPhyloTreePatient-method getPhyloTreePatient
getPhyloTreeRef getPhyloTreeRef
getPhyloTreeRef-method getPhyloTreeRef
getSampleInfo getSampleInfo
getSampleInfo-method getSampleInfo
getTree getTree
getTree-method getTree
getTreeMethod getTreeMethod
getTreeMethod-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 Run the default MesKit app for analysis locally
subMaf Subset Maf object
testNeutral testNeutral
triMatrix triMatrix
vafCluster vafCluster