tmb: Estimate Tumor Mutation Burden

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Estimate Tumor Mutation Burden

Description

Estimates Tumor Mutation Burden in terms of per megabases

Usage

tmb(
  maf,
  captureRegions = NULL,
  captureSize = 50,
  logScale = TRUE,
  ignoreCNV = TRUE,
  plotType = "classic",
  pointcol = "#2c3e50",
  verbose = TRUE
)

Arguments

maf	maf MAF object
captureRegions	capture regions. Default NULL. If provided sub-sets variants within the capture regions for TMB estimation. Can be a data.frame or a tsv with first three columns containing chromosome, start and end position.
captureSize	capture size for input MAF in MBs. Default 50MB. Mutually exclusive with captureRegions
logScale	Default TRUE. For plotting purpose only.
ignoreCNV	Default TRUE. Ignores all the variants annotated as 'CNV' in the 'Variant_Type' column of MAF
plotType	Can be "classic" or "boxplot". Set to 'NA' for no plot.
pointcol	Default #2c3e50
verbose	Default TRUE

Value

data.table with TMB for every sample

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
tmb(maf = laml)

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.