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#' Derive threshold for importance scores and return final networks.
#'
#' INPUT
#' out.iRafNet output from function iRafNet
#' out.perm output from function Run_permutation
#' TH FDR threshold
#'
#' @export
#"iRafNet_network" <- function(out, ...)UseMethod("iRafNet")
iRafNet_network <- function(out.iRafNet,out.perm,TH) {
M<-dim(out.perm)[2]; #-- number of permutations
j.np<-sort(out.iRafNet[,3],decreasing=TRUE)
FDR<-rep(0,dim(out.perm)[1]);
for (s in 1:length(j.np)){
FP<-sum(sum(out.perm>=j.np[s]))/M
FDR[s]<-FP/s;
if (FDR[s]>TH) {th<-j.np[s]; break;}
}
return(out.iRafNet[out.iRafNet[,3]>th,seq(1,2)])
}
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