Nothing
## __________________________________________________________
##
## FUNCTION BuildEdges
##
## Given a score matrix, this function builds the list of the
## edges of the associated network. Edges are ordered according
## to their scores.
##
## The score matrix has been computed from a network inference
## algorithm (e.g. DBNScoreStep1 or DBNScoreStep2, Shrinkage,
## Lasso, ...).
##
## An optional threshold can be specified, as well as a maximal
## number of edges.
##
##
## __________________________________________________________
##
BuildEdges <- function(score,threshold=1,nb=NULL,
targetNames=NULL,predNames=NULL,prec=3,dec=FALSE){
## ===============================================
## INITIALIZING
## _______________________________________________
r <- dim(score)[1] # nb of target genes
d <- dim(score)[2] # nb of predictor genes
## ===============================================
## BUILDING THE MATRIX OF EDGES
## _______________________________________________
## ordering the scores
scoreIdx <- order(score,decreasing=dec)
nbEdges <- min(nb,sum((score<threshold)*(dec==FALSE)+(score>threshold)*(dec==TRUE),na.rm=TRUE),length(scoreIdx))
## coordinate in the matrix
Pred <- ceiling(scoreIdx[1:nbEdges]/r)
Target <- scoreIdx[1:nbEdges]-(Pred-1)*r
## names if specified
if(!(is.null(predNames))){
Pred <- predNames[Pred]
}
if(!(is.null(targetNames))){
Target <- targetNames[Target]
}
## Returning the matrix of Edges
Score=round(score[scoreIdx][1:nbEdges],prec)
return(as.matrix(cbind(Pred,Target,Score)))
}
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