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, cohortName = NULL,
  tcga_cohorts = NULL, primarySite = FALSE, col = c("gray70",
  "black"), medianCol = "red")

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"

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.

medianCol

color for median line. Default red.

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 2.0.10 Index]