tcgaCompare: Compare mutation load against TCGA cohorts

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

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",
  decreasing = FALSE,
  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.
decreasing	Default FALSE. Cohorts are arranged in increasing mutation burden.
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")

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.