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. |
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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:
- Calculate the shortest path between the regulator node and each node in observed_regulation
- 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: