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Example of HHN with permuted networks #5

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jhrcook commented Oct 2, 2019

I have implemented an example use of Hierarchical HotNet that uses permuted networks for the statistical test instead of just the permuted node scores. It is derived from "examples/example_commands.sh" and the main changes were in the "Permute data." section. The script currently only uses 25 permutations instead of the 100 in the original file.

This PR is made in reference to a conversation on the Google Group with Matt in March (sorry for the delay)
https://groups.google.com/forum/#!topic/hotnet-users/hW1lN8Ok8tY

  • Josh Cook
jhrcook added 4 commits Oct 2, 2019
The file "./examples/example_commands_permhierarchies.sh" contains
a modified version of "./examples/example_commands.sh" using the
permutation of the network's edges for the test (instead of
permuting scores).

It runs completely (currently only using 25 permutations) only
printing a warning for a deprecation of a numpy method that is
used in "./src/hhio.py".
@matthewreyna

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matthewreyna commented Oct 2, 2019

Thanks for submitting this example, Josh! I'll add a shortcut (reuse the beta parameter from the observed network for each of the permuted networks instead of computing it for each of the permuted networks) and update the repository.

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