pylimma.prop_true_null

pylimma.prop_true_null(p, method='lfdr', nbins=20, **convest_kwargs)[source]

Estimate the proportion of null p-values.

Port of R limma’s propTrueNull. Dispatches to one of four estimators.

Parameters:

  • p (array_like) – Observed p-values.

  • method ({"lfdr", "mean", "hist", "convest"}, default "lfdr") – Estimator to use.

  • nbins (int, default 20) – Number of histogram bins when method="hist".

  • **convest_kwargs – Extra keyword arguments passed to convest() when method="convest".

Returns:

Estimated proportion of true nulls.

Return type:

float