plotApobecDiff {maftools} | R Documentation

## 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)

[Package maftools version 2.3.30 Index]