MAF {maftools} | R Documentation

## Construct an MAF object

### Description

Constructor function which takes non-synonymous, and synonymous variants along with an optional clinical information and generates an MAF object

### Usage

    MAF(nonSyn = NULL, syn = NULL, clinicalData = NULL, verbose = TRUE)

### Arguments

`nonSyn` | non-synonymous variants as a data.table or any object that can be coerced into a data.table (e.g: data.frame, GRanges)
`syn` | synonymous variants as a data.table or any object that can be coerced into a data.table (e.g: data.frame, GRanges)
`clinicalData` | Clinical data associated with each sample/Tumor_Sample_Barcode in MAF. Could be a text file or a data.frame. Requires at least a column with the name 'Tumor_Sample_Barcode' Default NULL.
`verbose` | Default TRUE

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml_dt = data.table::fread(input = laml.maf)
    laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #Clinical data
    # Just for demonstration
    nsyn_vars = laml_dt[Variant_Classification %in% "Missense_Mutation"]
    syn_vars = laml_dt[Variant_Classification %in% "Silent"]
    maftools::MAF(nonSyn = nsyn_vars, syn = syn_vars, clinicalData = laml.clin)

[Package maftools version 2.10.05 Index]