AberystwythSystemsBiology / AberystwythSystemsBiology/pyMEAN
Hypergeometric test from scipy does not have the right parameters fed
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Descripción
```python
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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