mutTrunkBranch {MesKit} | R Documentation

## mutTrunkBranch

### 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)

[Package MesKit version 1.4.0 Index]