get_mut_status: Converts MAF file into mutation matrix.

In ProgModule: Identification of Prognosis-Related Mutually Exclusive Modules

Converts MAF file into mutation matrix.

Description

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

Usage

get_mut_status(mutvariant, nonsynonymous = TRUE)

Arguments

mutvariant	A nx3 data frame of patients' somatic mutation data,the first line is gene symbol,the second line is sample ID and the third line is mutation classification.
nonsynonymous	Logical, tell if extract the non-synonymous 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

maf<-system.file("extdata","maffile.maf",package = "ProgModule")
maf_data<-read.delim(maf)
mutvariant<-maf_data[,c("Hugo_Symbol","Tumor_Sample_Barcode","Variant_Classification")]
#perform the function `get_mut_status`.
mut_status.example<-get_mut_status(mutvariant,nonsynonymous = TRUE)

ProgModule documentation built on May 29, 2024, 9:16 a.m.