getPhyloTree: getPhyloTree

Description Usage Arguments Value Examples

View source: R/getPhyloTree.R

Description

getPhyloTree

Usage

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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

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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.