get_mut_status: Converts MAF file or data in other formats into mutation...

In ssMutPA: Single-Sample Mutation-Based Pathway Analysis

Converts MAF file or data in other formats into mutation matrix.

Description

The function 'get_mut_status' is used to convert MAF file or data in other formats into a binary mutation matrix.

Usage

get_mut_status(maf_data, nonsynonymous = TRUE, TCGA = TRUE, mut_rate = 0)

Arguments

maf_data	The patients' somatic mutation data, which in MAF format or others.
nonsynonymous	Logical. Determine if extract the non-silent somatic mutations .
TCGA	Logical. Determine whether the file is in MAF format .
mut_rate	Used to filter genes with target mutation rate .

Value

A binary mutations matrix, in which 1 represents that a particular gene has mutated in a particular sample, and 0 represents that gene is wild type.

Examples

#load the data
mut_path <- system.file("extdata","mutation_data.Rdata",package = "ssMutPA")
load(mut_path)
#perform the function `get_mut_status`.
mut_status<-get_mut_status(mutation_data,nonsynonymous=TRUE,TCGA=TRUE,mut_rate=0)

ssMutPA documentation built on Oct. 16, 2024, 1:06 a.m.