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

## Documentation for package ‘MesKit’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calFst | calFst
calJSI | compareJSI
calNeiDist | calNeiDist
ccfAUC | ccfAUC
classifyMut | classifyMut
cna2gene | cna2gene
compareCCF | compareCCF
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
getPhyloTreeTsbLabel | getPhyloTreeRef
getPhyloTreeTsbLabel-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
mutCluster | mutCluster
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