vafCompare: compare VAF across two cohorts

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Draw boxplot distibution of VAFs across two cohorts

Usage

vafCompare(
  m1,
  m2,
  genes = NULL,
  top = 5,
  vafCol1 = NULL,
  vafCol2 = NULL,
  m1Name = "M1",
  m2Name = "M2",
  cols = c("#2196F3", "#4CAF50"),
  sigvals = TRUE,
  nrows = NULL,
  ncols = NULL
)

Arguments

m1	first MAF object. Required.
m2	second MAF object. Required.
genes	specify genes for which plot has to be generated. Default NULL.
top	if genes is NULL plots top n number of genes. Defaults to 5.
vafCol1	manually specify column name for vafs in m1. Default looks for column 't_vaf'
vafCol2	manually specify column name for vafs in m2. Default looks for column 't_vaf'
m1Name	optional name for first cohort
m2Name	optional name for second cohort
cols	vector of colors corresponding to m1 and m2 respectivelly.
sigvals	Estimate and add significance stars. Default TRUE.
nrows	Number of rows in the layout. Default NULL - estimated automatically
ncols	Number of genes drawn per row. Default 4

maftools documentation built on Feb. 6, 2021, 2 a.m.