tcgaCompare: Compare mutation load against TCGA cohorts

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

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 = 35.8,
  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,
  rm_zero = TRUE,
  cohortFontSize = 0.8,
  axisFontSize = 0.8
)

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 35.8 mb.
tcga_capture_size	capture size for TCGA cohort in MB. Default 35.8. Do NOT change. See details for more information.
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
rm_zero	Remove samples with zero mutations? Default TRUE
cohortFontSize	Default 0.8
axisFontSize	Default 0.8

Details

Tumor mutation burden for TCGA cohorts is obtained from TCGA MC3 study. For consistency TMB is estimated by restricting variants within Agilent Sureselect capture kit of size 35.8 MB.

Value

data.table with median mutations per cohort

Source

TCGA MC3 file was obtained from https://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc. See TCGAmutations R package for more details. Further downstream script to estimate TMB for each sample can be found in ‘inst/scripts/estimate_tcga_tmb.R’

References

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines Kyle Ellrott, Matthew H. Bailey, Gordon Saksena, et. al. Cell Syst. 2018 Mar 28; 6(3): 271–281.e7. https://doi.org/10.1016/j.cels.2018.03.002

Examples

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

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