R/prepResult.R

In SCORPION: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks

prepResult <- function(zScale, output, regulatoryNetwork, geneCoreg, tfCoopNetwork, edgelist, motif){
  resList <- list()
  numGenes = dim(geneCoreg)[1]
  numTFs   = dim(tfCoopNetwork)[1]
  numEdges = sum(regulatoryNetwork!=0)
  # if (!zScale){
  #   regulatoryNetwork <- stats::pnorm(regulatoryNetwork)
  #   geneCoreg         <- stats::pnorm(geneCoreg)
  #   tfCoopNetwork     <- stats::pnorm(tfCoopNetwork)
  # }
  # if("regulatory"%in%output){
  #   # if(edgelist){
  #   #   regulatoryNetwork <- melt.array(regulatoryNetwork)
  #   #   colnames(regulatoryNetwork) <- c("TF", "Gene", "Score")
  #   #   regulatoryNetwork$Motif <- as.numeric(with(regulatoryNetwork, paste0(TF, Gene))%in%paste0(motif[,1],motif[,2]))
  #   # }
  #   resList$regNet <- regulatoryNetwork
  # }
  # if("coexpression"%in%output){
  #   # if(edgelist){
  #   #   geneCoreg <- melt.array(geneCoreg)
  #   #   colnames(geneCoreg) <- c("Gene.x", "Gene.y", "Score")
  #   # }
  #   resList$coregNet <- geneCoreg
  # }
  # if("cooperative"%in%output){
  #   # if(edgelist){
  #   #   tfCoopNetwork <- melt.array(tfCoopNetwork)
  #   #   colnames(tfCoopNetwork) <- c("TF.x", "TF.y", "Score")
  #   # }
  #   resList$coopNet <- tfCoopNetwork
  # }
  list(regNet=regulatoryNetwork, coregNet=geneCoreg, coopNet=tfCoopNetwork, numGenes=numGenes, numTFs=numTFs, numEdges=numEdges)
}