triMatrix: triMatrix

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

Description

Calculate the frequency of 96 trinucleotide mutation based on somatic SNVs.

Usage

triMatrix(phyloTree, patient.id = NULL, level = 2)

Arguments

phyloTree	phyloTree or phyloTreeList object generated by getPhyloTree function.
patient.id	Select the specific patients. Default NULL, all patients are included
level	Calculate the frequency of 96 trinucleotide mutatio on different levels. 1: patient-level, 2: tumor-level, 3: sample-level, 4: branch-level, 5: shared pattern (public/shared/private) of each tumor. 6: trunk/branch-level. Default 2.

Value

The frequency of 96 trinucleotide mutation.

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')
triMatrix(phyloTree)

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