pylimma.gene_set_test

pylimma.gene_set_test(index, statistics, alternative='mixed', type='auto', ranks_only=True, nsim=9999, rng=None)

Competitive gene-set test.

Port of R limma’s geneSetTest. When ranks_only=True the p-value is obtained analytically via rank_sum_test_with_correlation(); otherwise a permutation distribution is simulated using rng.

The type keyword shadows the Python builtin type; this is deliberate for R-signature parity (limma’s geneSetTest(type=...)). The shadow is local to this function and the body never invokes type(); callers keyword-passing type=... works as expected.

Return type:

float

Parameters:

• statistics (ndarray)

• alternative (str)

• type (str)

• ranks_only (bool)

• nsim (int)