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surh / Anchurus

Analyzing SNPs in metagenomes
GNU General Public License v3.0
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Permutation test on hypergeometric test makes wrong comparison. #3

Closed surh closed 6 years ago

surh commented 6 years ago

Using the permutation on the --test hg of MKtest.py uses the odds ratio of scipy.stats Fisher's exact test. The way the contingency matrix is passed right now, uses the (Pn/Ps) / (Dn/Ds) ratio instead of the (Dn/Ds) / (Pn/Ps) ratio, which means that the test is not really interpretable.

surh commented 6 years ago

This is now fixed by pull request https://github.com/surh/Anchurus/pull/6