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andreas-wilm/fisher_pv_comb.py

Created November 18, 2015 09:10
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Fisher's method for combining p-values
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fisher_pv_comb.py
from math import log
from scipy import stats
def fisher_comb(pv1, pv2):
"""
Fisher's method for combining p-values:
https://en.wikipedia.org/wiki/Fisher's_method
See for example breseq-0.18b:polymorphism_statistics.r
For CDF use see http://stackoverflow.com/questions/11725115/p-value-from-chi-sq-test-statistic-in-python
"""
comb_log = -2.0 * (log(pv1) + log(pv2))
comb_pv = 1.0 - stats.chi2.cdf(comb_log, 4)
return comb_pv
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  • This function is limited to two pvalues
  • just use scipy.stats.combine_pvalues()

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