get_mutual_module {ProgModule} | R Documentation |
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
)
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. |
Value
The mutually exclusive module.
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)
[Package ProgModule version 0.1.0 Index]