[FEATURE] Estimation of pi0 and lfdr/PEP by Storey's methods

PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

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[FEATURE] Estimation of pi0 and lfdr/PEP by Storey's methods #11

Closed grosenberger closed 6 years ago

grosenberger commented 6 years ago

This PR implements support for estimation of pi0 and lfdr/PEP by Storey's methods. The implementation follows the Bioconductor/qvalue R code, although with kernel density estimators and spline fitting functions provided by SciPy introducing slight differences.

cosmo-ethz commented 6 years ago

@cosmo-ethz is @uweschmitt, sorry for the confusion.

grosenberger commented 6 years ago

Thanks for the review. I just realized that the changes are not yet compatible with pyprophet-cli, so I will make a PR there as well before we merge.