CausalR

An implementation of the CausalR algorithm described by [Bradley2017].

[Bradley2017]Bradley, G., & Barrett, S. J. (2017). CausalR - extracting mechanistic sense from genome scale data. Bioinformatics, (June), 1–3.
pybel_tools.analysis.causalr.rank_causalr_hypothesis(graph, node_to_regulation, regulator_node)[source]

Test the regulator hypothesis of the given node on the input data using the algorithm.

Note: this method returns both +/- signed hypotheses evaluated

Algorithm:

  1. Calculate the shortest path between the regulator node and each node in observed_regulation
  2. Calculate the concordance of the causal network and the observed regulation when there is path between target node and regulator node
Parameters:
  • graph (networkx.DiGraph) – A causal graph
  • node_to_regulation (dict) – Nodes to score (1,-1,0)
Return Dictionaries with hypothesis results (keys:
 

score, correct, incorrect, ambiguous)
Return type:

dict