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vafCompare

compare VAF across two cohorts

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

Summarize, Analyze and Visualize MAF Files

v2.6.05
MIT + file LICENSE
Authors
Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)
Initial release
2015-12-14

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