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

Description Usage Arguments Details Value See Also Examples

View source: R/plotApobecDiff.R

Description

Plots differences between APOBEC enriched and non-APOBEC enriched samples

Usage

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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

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## 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)

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