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
- (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).
- Gene Summary (txt)
- Sample Summary (txt)
- Summary (txt)
- Clinical Data (txt)
- Maftools Output (maf)
- Summary plots (png)
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")
library("maftools")
library("RColorBrewer")
library("R.utils")