## ---- eval=FALSE---------------------------------------------------------
##         library(CoRegNet)
##         data(CIT_BLCA_EXP,HumanTF,CIT_BLCA_Subgroup)
##         dim(CIT_BLCA_EXP)
##         #showing 6 first TF in the gene expression dataset
##         head(intersect(rownames(CIT_BLCA_EXP),HumanTF))

## ---- eval=FALSE---------------------------------------------------------
## 	grn = hLICORN(CIT_BLCA_EXP, TFlist=HumanTF)

## ---- eval=FALSE---------------------------------------------------------
## 	influence = regulatorInfluence(grn,CIT_BLCA_EXP)

## ---- eval=FALSE---------------------------------------------------------
## 	coregs= coregulators(grn)

## ---- eval=FALSE---------------------------------------------------------
## 	display(grn,CIT_BLCA_EXP,influence,clinicalData=CIT_BLCA_Subgroup)

## ---- eval=FALSE---------------------------------------------------------
##     # An example of how to infer a co-regulation network
##     grn =hLICORN(CIT_BLCA_EXP, TFlist=HumanTF)
##     print(grn)

## ---- eval=FALSE---------------------------------------------------------
##     #Default discretization.
##     #Uses the standard deviation of the whole dataset to set a threshold.
##     disc1=discretizeExpressionData(CIT_BLCA_EXP)
##     table(disc1)
##     boxplot(as.matrix(CIT_BLCA_EXP)~disc1)
## 
##     #Discretization with a hard threshold
##     disc2=discretizeExpressionData(CIT_BLCA_EXP, threshold=1)
##     table(disc2)
##     boxplot(as.matrix(CIT_BLCA_EXP)~disc2)
## 
##     # more examples here
##     help(discretizeExpressionData)

## ---- eval=FALSE---------------------------------------------------------
## # running only on the 200 first gene in the matrix for fast analysis
##     # Choosing to divide in 4 threads whenever possible
##     options("mc.cores"=4)
##     grn =hLICORN(head(CIT_BLCA_EXP,200), TFlist=HumanTF)
##     print(grn)
##     options("mc.cores"=2)
##     grn =hLICORN(head(CIT_BLCA_EXP,200), TFlist=HumanTF)
##     print(grn)

## ---- eval=FALSE---------------------------------------------------------
##     # ChIP data from the CHEA database
##     data(CHEA_sub)
## 
##     #ChIP data from the ENCODE project
##     data(ENCODE_sub)
## 
##     # Protein protein interactions between TF from the HIPPIE database
##     data(HIPPIE_sub)
## 
##     # Protein protein interactions between TF from the STRING database
##     data(STRING_sub)
## 
##     enrichedGRN = addEvidences(grn,CHEA_sub,ENCODE_sub)
##     enrichedGRN = addCooperativeEvidences(enrichedGRN,HIPPIE_sub,STRING_sub)

## ---- eval=FALSE---------------------------------------------------------
##     print(enrichedGRN)

## ---- eval=FALSE---------------------------------------------------------
##         # Default unsupervised refinement method
##     refinedGRN = refine(enrichedGRN)
##     print(refinedGRN)
##     # Example of supervised refinement with the CHEA chip data
##     refinedGRN = refine(enrichedGRN, integration="supervised",
##             referenceEvidence="CHEA_sub")
##     print(refinedGRN)

## ---- eval=FALSE---------------------------------------------------------
##     CITinf =regulatorInfluence(grn,CIT_BLCA_EXP)
## 

## ---- eval=FALSE---------------------------------------------------------
##     # Coregulators of a hLICORN  inferred network
##     head(coregulators(grn))

## ---- eval=FALSE---------------------------------------------------------
##     data(CIT_BLCA_CNV)
##     data(CIT_BLCA_Subgroup)

## ---- eval=FALSE---------------------------------------------------------
##     display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf)

## ---- eval=FALSE---------------------------------------------------------
##     # Visualizing additional regulatory or co-regulatory evidences in the network
##     display(enrichedGRN,expressionData=CIT_BLCA_EXP,TFA=CITinf)
## 
## 
##     # Visualizing sample classification using a named factor
##     display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf,clinicalData=CIT_BLCA_Subgroup)
## 
##     # Visualizing copy number alteration of regulators
##     data(CIT_BLCA_CNV)
##     display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf,clinicalData=CIT_BLCA_Subgroup,alterationData=CIT_BLCA_CNV)
##