ProgModule (version 0.1.0)

get_mutual_module: Extract the mutually exclusive module.

Description

The function `get_mutual_module` is used to determine if neighbor genes should be added to the module by calculating the score.

Usage

get_mutual_module(
  module,
  net,
  freq_matrix,
  sur,
  module_sig,
  univarCox_result,
  rate
)

Value

The mutually exclusive module.

Arguments

module

The Original modular gene set.

net

The local network extracted from PPI network.

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.

module_sig

A label for whether the module is a risk factor or a protective factor for survival.

univarCox_result

The result of Cox univariate analysis,generated by `get_univarCox_result`.

rate

The rate of increase in score,default is 0.05.

Examples

#load the data
data(mut_status)
sur<-system.file("extdata","sur.csv",package = "ProgModule")
sur<-read.delim(sur,sep=",",header=TRUE,row.names = 1)
data(net)
data(module)
data(univarCox_result)
#perform the function `get_mutual_module`.
mutuallyexclusivemodule.example<-get_mutual_module(module,net,freq_matrix=mut_status,sur,
module_sig="risk",univarCox_result,rate=0.05)