get_mut_matrix: Converts MAF into mutation matrix.

In pathwayTMB: Pathway Based Tumor Mutational Burden

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
)

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.

Value

The survival-related mutations matrix.

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)

pathwayTMB documentation built on Aug. 9, 2022, 5:09 p.m.