maftools-in-R

maftools is a bioinformatic package use to annotate mutations and find variants. Full documentation can be found online.

https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html

FILE INPUTS

• (required) MAF file - can be gz compressed.
• (optional) clinical data associated with each sample/Tumor_Sample_Barcode in MAF.
• (optional) copy number data if available. Can be GISTIC output or a custom table containing sample names, gene names and copy-number status (Amp or Del).

FILE OUTPUTS

• Gene Summary (txt)
• Sample Summary (txt)
• Summary (txt)
• Clinical Data (txt)
• Maftools Output (maf)
• Summary plots (png)

PACKAGE REQUIREMENTS

Install required libraries from Bioconductor

Run this code if the packages are not already installed

if (!require("BiocManager"))
  install.packages("BiocManager")
BiocManager::install("maftools")

install.packages("R.utils")

Load required libraries

library("maftools")
library("RColorBrewer")
library("R.utils")