tcgaCompare {maftools}R Documentation

Compare mutation load against TCGA cohorts

Description

Compares mutation load in input MAF against all of 33 TCGA cohorts

Usage

tcgaCompare(maf, capture_size = NULL, cohortName = NULL,
  primarySite = FALSE, col = c("gray70", "black"), medianCol = "red",
  fn = NULL, width = 8, height = 5, fontSize = 10)

Arguments

maf

an MAF object 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.

cohortName

name for the input MAF cohort. Default "Input"

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.

medianCol

color for median line. Default red.

fn

If provided saves plot to output pdf with basename fn. Default NULL.

width

width for output plot

height

height of output plot

fontSize

base fontsize. Default 10.

Value

ggplot object

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 1.8.0 Index]