getPhyloTree: getPhyloTree

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

Description

getPhyloTree

Usage

getPhyloTree(
  maf,
  patient.id = NULL,
  method = "NJ",
  min.vaf = 0,
  min.ccf = 0,
  bootstrap.rep.num = 100,
  ...
)

Arguments

maf	Maf or MafList object generated by readMaf function
patient.id	Select the specific patients. Default NULL, all patients are included.
method	Approach to construct phylogenetic trees. Choose one of "NJ"(Neibor-Joining), "MP"(maximum parsimony), "ML"(maximum likelihood), "FASTME.ols" or "FASTME.bal".
min.vaf	The minimum value of vaf. Default 0.
min.ccf	The minimum value of CCF. Default 0
bootstrap.rep.num	Bootstrap iterations. Default 100.
...	Other options passed to subMaf

Value

PhyloTree or phyloTreeList object

Examples

maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
phyloTree <- getPhyloTree(maf)

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