plotApobecDiff: Plot differences between APOBEC enriched and non-APOBEC...

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

Plot differences between APOBEC enriched and non-APOBEC enriched samples.

Description

Plots differences between APOBEC enriched and non-APOBEC enriched samples

Usage

plotApobecDiff(
  tnm,
  maf,
  pVal = 0.05,
  title_size = 1,
  axis_lwd = 1,
  font_size = 1.2
)

Arguments

tnm	output generated by trinucleotideMatrix
maf	an MAF object used to generate the matrix
pVal	p-value threshold for fisher's test. Default 0.05.
title_size	size of title. Default 1.3
axis_lwd	axis width. Default 1
font_size	font size. Default 1.2

Details

Plots differences between APOBEC enriched and non-APOBEC enriched samples (TCW). Plot includes differences in mutations load, tCw motif distribution and top genes altered.

Value

list of table containing differenatially altered genes. This can be passed to forestPlot to plot results.

See Also

trinucleotideMatrix plotSignatures

Examples

## Not run: 
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', prefix = 'chr',
add = TRUE, useSyn = TRUE)
plotApobecDiff(laml.tnm)

## End(Not run)

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