tcgaCompare {maftools} | R Documentation

## Compare mutation load against TCGA cohorts

### Description

Compares mutation load in input MAF against all of 33 TCGA cohorts

### Usage

    tcgaCompare(maf, capture_size = NULL, cohortName = NULL,
      primarySite = FALSE, col = c("gray70", "black"), medianCol = "red",
      fn = NULL, width = 8, height = 5, fontSize = 10)

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`capture_size` | capture size for input MAF in MBs. Default NULL. If provided plot will be scaled to mutations per mb. TCGA capture size is assumed to be 50mb.
`cohortName` | name for the input MAF cohort. Default "Input"
`primarySite` | If TRUE uses primary site of cancer as labels instead of TCGA project IDs. Default FALSE.
`col` | color vector for length 2 TCGA cohorts and input MAF cohort. Default gray70 and black.
`medianCol` | color for median line. Default red.
`fn` | If provided saves plot to output pdf with basename fn. Default NULL.
`width` | width for output plot
`height` | height of output plot
`fontSize` | base fontsize. Default 10.

### Value

ggplot object

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    tcgaCompare(maf = laml, cohortName = "AML")

[Package maftools version 1.8.0 Index]