Determining Edges More Progress on Network Inference

Lately, I have been writing an R script to infer network using in silico data. Last version of the script was reading MIDAS file and plotting expression profiles. I have modified it and now it reads MIDAS file, does some analyses and prints causal relations to a file. This file is a SIF file as required. This dataset is generated with 20 antibodies but only 3 of them are perturbed. Also, for one, stimulus is missing.