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Hypergeometric test from scipy does not have the right parameters fed #2

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Marie-anneMawhin opened this issue Apr 27, 2022 · 0 comments

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@Marie-anneMawhin
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p_value = 1-hypergeom.cdf(
  num_hits-1,
  population-num_dbids,
  num_cpds,
  num_dbids)

According to scipy doc: cdf or sf take for argument : (k, M, n, N, loc=0) where M is the total number of objects (and not n=N-m like in R phyper, so here it should be the population.
Also the fisher_exact test could take an alternative param 'greater' so that both p-value would be the same, as Fischer is based on hypergeometric distribution.
I hope this package is still maintain :)

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