maf2matrix {survtype}R Documentation

Convert a MAF file to a mutation matrix

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)

[Package survtype version 1.8.0 Index]