tcgaCompare {maftools}R Documentation

Compare mutation load against TCGA cohorts

Description

Compares mutation load in input MAF against all of 33 TCGA cohorts derived from MC3 project.

Usage

tcgaCompare(
  maf,
  capture_size = NULL,
  tcga_capture_size = 50,
  cohortName = NULL,
  tcga_cohorts = NULL,
  primarySite = FALSE,
  col = c("gray70", "black"),
  bg_col = c("#EDF8B1", "#2C7FB8"),
  medianCol = "red",
  logscale = TRUE,
  rm_hyper = FALSE
)

Arguments

maf

MAF object(s) generated by read.maf

capture_size

capture size for input MAF in MBs. Default NULL. If provided plot will be scaled to mutations per mb. TCGA capture size is assumed to be 50mb.

tcga_capture_size

capture size for TCGA cohort in MB. Default 50

cohortName

name for the input MAF cohort. Default "Input"

tcga_cohorts

restrict tcga data to these cohorts.

primarySite

If TRUE uses primary site of cancer as labels instead of TCGA project IDs. Default FALSE.

col

color vector for length 2 TCGA cohorts and input MAF cohort. Default gray70 and black.

bg_col

background color. Default'#EDF8B1', '#2C7FB8'

medianCol

color for median line. Default red.

logscale

Default TRUE

rm_hyper

Remove hyper mutated samples (outliers)? Default FALSE

Value

data.table with median mutations per cohort

Examples

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

[Package maftools version 2.2.10 Index]