maf2matrix: Convert a MAF file to a mutation matrix

In survtype: Subtype Identification with Survival Data

Description

Create a mutation matrix using variant types

Usage

maf2matrix(maf, surv.data = NULL, sample.name = "Tumor_Sample_Barcode",
           gene.name = "Hugo_Symbol", variant.type = "Variant_Classification")

Arguments

maf	a MAF file
surv.data	survival data for sample names (default: NULL)
sample.name	the column name containing sample names (defult: "Tumor_Sample_Barcode")
gene.name	the column name containing gene names (defult: "Hugo_Symbol")
variant.type	the column name containing variant types (defult: "Variant_Classification")

Value

a mutation matrix

Author(s)

Dongmin Jung

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml.maf <- read.csv(laml.maf, sep = "\t")
laml.mat <- maf2matrix(laml.maf)

survtype documentation built on Nov. 8, 2020, 7:24 p.m.