Network concordance algorithm - Githubissues

pybel / pybel-tools

A PyBEL extension for analyzing BEL graphs

http://pybel-tools.readthedocs.io/

MIT License

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Network concordance algorithm #110

Closed cthoyt closed 7 years ago

cthoyt commented 7 years ago

Overlay differential gene expression. Apply cutoff for significantly up-regulated, down-regulated, and un-regulated genes
Look for statements that match (up-regulated increases up-regulated, up-regulated decreases down-regulated, etc.)
Calculate summary statistics over network

Couple to a pipeline for stratifying a graph by an annotation (neurommsig subgraph usually) then provide total summary.

What's the distribution of correct/(correct + incorrect + ambiguous) over all subgraphs?

[x] Implement calculation
[x] Implement pipeline with annotation stratification
[x] Implement p-value checking by taking random subsamples of graph (90%, 10 times, or whatever parameters)