mutTrunkBranch: mutTrunkBranch

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

Description

Summarize and conduct paired Fisher test of mutations of trunk/branches in a phylogenetic tree.

Usage

mutTrunkBranch(
  phyloTree,
  patient.id = NULL,
  CT = FALSE,
  pvalue = 0.05,
  plot = TRUE
)

Arguments

phyloTree	phyloTree or phyloTreeList object generated by getPhyloTree function.
patient.id	Select the specific patients. Default NULL, all patients are included
CT	Distinction between C>T at CpG and C>T at other sites. (Default: FALSE).
pvalue	Confidence level of the interval for Fisher test. Default 0.05.
plot	Logical. (Default: TRUE).

Value

a list of box plots based on mutational categories

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")

## Load a reference genome.
library(BSgenome.Hsapiens.UCSC.hg19)

phyloTree <- getPhyloTree(maf, patient.id = 'V402')
mutTrunkBranch(phyloTree, plot = TRUE)

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