get_mut_status {PMAPscore}

Converts MAF file into mutation matrix

Description

The function 'get_mut_status' uses to convert MAF file into mutation matrix.

Usage

get_mut_status(maf_data, nonsynonymous = TRUE)

Arguments

maf_data

The patients' somatic mutation data, which in MAF format.

nonsynonymous

Logical, tell if extract the non-silent somatic mutations (nonsense mutation, missense mutation, frame-shif indels, splice site, nonstop mutation, translation start site, inframe indels).

Value

A binary mutations matrix, in which 1 represents that a particular gene has mutated in a particular sample, and 0 represents that gene has no mutation in a particular sample .

Examples

#load the data
data(maf_data)
#perform the function `get_mut_status`.
mutmatrix.example<-get_mut_status(maf_data,nonsynonymous = TRUE)