inst/doc/EdgeticDriver_exam.R

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

### R code from vignette source 'EdgeticDriver_exam.Rnw'

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### code chunk number 1: EdgeticDriver
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library(EdgeticDriver)


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### code chunk number 2: EdgeticDriver
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#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")


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### code chunk number 3: EdgeticDriver
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#Identifying the dysregulated edges between cancer and normal samples
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")
#identify the dysregulated edges
DysCN=EdgeticDys_CN(Input.exp,Network,thr=0.01)


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### code chunk number 4: EdgeticDriver
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#Identifying the dysregulated edges among cancer samples
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")
#identify the dysregulated edges
Input.exp=Input.exp[,Cancer_s]
DysC=EdgeticDys_CN(Input.exp,Network,thr=0.01)


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### code chunk number 5: EdgeticDriver
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#Identifying the dysregulated edges in both two conditions
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")
#identify the dysregulated edges
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)

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### code chunk number 6: EdgeticDriver
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#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)

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### code chunk number 7: sessionInfo
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sessionInfo()