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Example of HHN with permuted networks #5
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)
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".