plotApobecDiff: Plot differences between APOBEC enriched and non-APOBEC...
In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Details Value See Also Examples

Plots differences between APOBEC enriched and non-APOBEC enriched samples

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

`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

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

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

trinucleotideMatrix plotSignatures

## 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)