def test_fdr(self):
"""Test function fdr"""
fdr(pvals)
fdr(pvals, alpha=.01, method='negcorr')
fdr(pvals2)
fdr(pvals2, alpha=.90, method='negcorr')
# Wrong arguments
with pytest.raises(ValueError):
fdr(pvals, method='wrong')
def test_fdr(self):
"""Test function fdr.
Compare to the p.adjust R function.
"""
# FDR BH
# ------
reject, pval_corr = fdr(pvals)
assert_array_equal(reject, [False, False, True, False, False])
assert_array_almost_equal(pval_corr, [0.52, .175, .0005, .075, .175])
# With NaN values
_, pval_corr = fdr(pvals2_NA)
assert_array_almost_equal(pval_corr, [.52, np.nan, .28, .40, .28])
# With 2D arrays
_, pval_corr = fdr(pvals_2d)
pval_corr = np.round(pval_corr.ravel(), 3)
assert_array_almost_equal(
pval_corr,
[.52, .21, .001, .135, .21, .52, np.nan, .21, 0.386, .21])
# FDR BY
# ------
reject, pval_corr = fdr(pvals, method='fdr_by')
assert_array_equal(reject, [False, False, True, False, False])
assert_array_almost_equal(
pval_corr,
[1., 0.399583333, 0.001141667, 0.171250000, 0.399583333])
# With NaN values
_, pval_corr = fdr(pvals2_NA, method='fdr_by')
assert_array_almost_equal(pval_corr,
[1., np.nan, 0.5833333, 0.8333333, .5833333])
# With 2D arrays
_, pval_corr = fdr(pvals_2d, method='fdr_by')
pval_corr = np.round(pval_corr.ravel(), 3)
assert_array_almost_equal(
pval_corr,
[1., 0.594, 0.003, 0.382, 0.594, 1., np.nan, 0.594, 1., 0.594])