MAF: Construct an MAF object

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

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)

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.