getEdgeticDriver: Identify the edgetic driver mutations

In lyshaerbin/EdgeticDriver: Identification of edgetic driver mutations by integrating gene expression and protein interaction network

Description

Identify the driver mutations that perturbe the protein interaction network

Usage

#Identifying the mutation mediated-dysregulated edges in both two conditions
#obtain the data for gene expression.
Input.exp=GetExampleData(exampleData="Exp.input")
# view first rows of data
head(Input.exp)
#obtain the sample label
Cancer_s=GetExampleData(exampleData="Cancer_s")
Normal_s=GetExampleData(exampleData="Normal_s")
#obtain the protein interaction network
Network=GetExampleData(exampleData="network")
#obtain the mutation data
Mut=GetExampleData(exampleData="mut")
DysCN=EdgeticDys_CN(Input.exp,Network,thr=0.01)
Input.exp2=Input.exp[,Cancer_s]
DysC=EdgeticDys_CN(Input.exp2,Network,thr=0.01)
Dys.net=EdgeticDys_both(DysCN,DysC)
Driver.mut=getEdgeticDriver(Dys.net,Mut,alpha=0.05,n.sim=1000)

Arguments

Dysnet	Dysregulated network for samples
Mut	The mutation files for samples
alpha	The significance level
n.sim	The simulation times defined by users

Value

MutPPI the mutation perturbed PPIs in cancer samples

lyshaerbin/EdgeticDriver documentation built on May 27, 2019, 8:45 a.m.