pathwayTMB (version 0.1.3)

get_mut_matrix: Converts MAF into mutation matrix.

Description

The function `get_mut_matrix` converts mutation annotation file (MAF) format data into a mutations matrix.Then use the fisher exact test to select the geneset with higher mutation frequency in alive sample group.Finally return the higher mutation frequency matrix.

Usage

get_mut_matrix(
  maffile,
  is.TCGA = TRUE,
  mut_fre = 0,
  nonsynonymous = TRUE,
  cut_Cox.pval = 1,
  cut_HR = 1,
  sur
)

Value

The survival-related mutations matrix.

Arguments

maffile

Input mutation annotation file (MAF) format data. It must be an absolute path or the name relatived to the current working directory.

is.TCGA

Is input MAF file from TCGA source. If TRUE uses only first 15 characters from Tumor_Sample_Barcode.

mut_fre

A threshold value(zero as the default value). The genes with a given mutation frequency equal or greater than the threshold value are retained for the following analysis.

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).

cut_Cox.pval

The significant cut_off pvalue for the univariate Cox regression.

cut_HR

The cut_off HR for the univariate Cox regression, uses to select the genes with survival benefit mutations.

sur

A nx2 data frame of samples' survival data,the first line is samples' survival event and the second line is samples' overall survival.

Examples

#get the path of the mutation annotation file and samples' survival data
maf<-system.file("extdata","data_mutations_extended.txt",package = "pathwayTMB")
sur_path<-system.file("extdata","sur.csv",package = "pathwayTMB")
sur<-read.csv(sur_path,header=TRUE,row.names = 1)
#perform the function 'get_mut_matrix'
mut_matrix<-get_mut_matrix(maffile=maf,mut_fre = 0.01,is.TCGA=FALSE,sur=sur)