get_Pvalue_S {ProgModule}

Get perturbed p-value.

Description

The function 'get_Pvalue_S' is used to calculate the perturbed p-value.

Usage

get_Pvalue_S(module, freq_matrix, sur, perms = 1000, local_network)

Arguments

module

The candidate module,generated by 'get_candidate_module'.

freq_matrix

The mutations matrix,generated by 'get_mut_status'.

sur

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

perms

The perturbation number,default is 1000.

local_network

The local network gene sets,generated by 'get_local_network'.

Value

Perturbed p-value.

Examples

#load the data
data(local_network)
data(mut_status)
data(candidate_module)
sur<-system.file("extdata","sur.csv",package = "ProgModule")
sur<-read.delim(sur,sep=",",header=TRUE,row.names = 1)
#perform the function `get_Pvalue_S`.
turbulence.example<-get_Pvalue_S(module=candidate_module,freq_matrix=mut_status,
sur=sur,perms=100,local_network)