get_PTMB {pathwayTMB}

Calculate the Pathway-based Tumor Mutational Burden.

Description

The function 'get_PTMB' uses to calculate the Pathway-based Tumor Mutational Burden (PTMB). PTMB is defined as pathway-based tumor mutational burden corrected by genes’ length and number.

Usage

get_PTMB(freq_matrix, genesmbol, path_mut_cutoff = 0, gene_path)

Arguments

freq_matrix

The mutations matrix,generated by 'get_mut_matrix'.

genesmbol

The genes' length matrix,generated by 'get_gene_length'.

path_mut_cutoff

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

gene_path

User input pathways geneset list.

Value

Return the Pathway-based Tumor Mutational Burden 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)
#perform the function `get_PTMB`
PTMB_matrix<-get_PTMB(freq_matrix=mut_matrix,genesmbol=genesmbol,gene_path=gene_path)