compareTree: compareTree

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

Description

Compares two phylogenetic trees and returns a detailed report of several distance methods

Usage

compareTree(
  phyloTree1,
  phyloTree2,
  plot = FALSE,
  min.ratio = 1/20,
  show.bootstrap = FALSE,
  use.tumorSampleLabel = FALSE
)

Arguments

phyloTree1	A phyloTree object generated by getPhyloTree function.
phyloTree2	A phyloTree object generated by getPhyloTree function.
plot	Logical (Default: FALSE). If TRUE, two trees will be plotted on the same device and their similarities will be shown.
min.ratio	Double, Default 1/20. If min.ratio is not NULL, all edge length which are smaller than min.ratio*the longest edge length will be reset as min.ratio*longest edge length.
show.bootstrap	Logical (Default: FALSE). Whether to add bootstrap value on internal nodes.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.

Value

A vector containing the following tree distance methods by R package phangorn Symmetric.difference Robinson-Foulds distance KF-branch distance the branch score distance (Kuhner & Felsenstein 1994) Path.difference difference in the path length, counted as the number of branches Weighted.path.difference difference in the path length, counted using branches lengths

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")


phyloTree1 <- getPhyloTree(maf$V402, method = "NJ")
phyloTree2 <- getPhyloTree(maf$V402, method = "MP")
compareTree(phyloTree1, phyloTree2)
compareTree(phyloTree1, phyloTree2, plot = TRUE)

Niinleslie/MesKit documentation built on Jan. 29, 2022, 10:24 a.m.