This actually brings up a decision point - in CRC, they use only the top 100 cliques by out-degree score to calculate the clique proportions. The cliques seem largely redundant, but I don't know how likely this is to miss variable CRC members between samples or groups. May be worth providing a parameter to allow tweaking of this threshold.
This is actually probably the part I am least sure about.
Probably worth reading the networkx docs on cliques.
Input will be a networkx network object (probably?, depends on Stage 3 choice) composed solely of SE-associated TF genes. No downstream targets.
Output in format like (A549_CRCs_CLIQUE_SCORES_DEGREE.txt from CRC):
Last column is out-degree score.
This actually brings up a decision point - in CRC, they use only the top 100 cliques by out-degree score to calculate the clique proportions. The cliques seem largely redundant, but I don't know how likely this is to miss variable CRC members between samples or groups. May be worth providing a parameter to allow tweaking of this threshold.