def apply(self):
self.clear()
self.progressBarInit()
self.filter_enabled(False)
self.words = [i.name for i in self.selected_data_transformed.domain.attributes]
self.p_values = hypergeom_p_values(self.data.X, self.selected_data_transformed.X, callback=self.progress)
self.fdr_values = false_discovery_rate(self.p_values)
self.filter_and_display()
self.filter_enabled(True)
self.progressBarFinished()
def test_false_discovery_rate(self):
p_values = np.array(
[0.727, 0.281, 0.791, 0.034, 0.628, 0.743, 0.958, 0.552, 0.867, 0.606,
0.611, 0.594, 0.071, 0.517, 0.526, 0.526, 0.635, 0.932, 0.210, 0.636])
# calculated with http://www.sdmproject.com/utilities/?show=FDR
fdr_fixed = np.array(
[0.92875, 0.9085714, 0.9305882, 0.68, 0.9085714, 0.92875, 0.958, 0.9085714,
0.958, 0.9085714, 0.9085714, 0.9085714, 0.71, 0.9085714, 0.9085714, 0.9085714,
0.9085714, 0.958, 0.9085714, 0.9085714]
)
corrected = false_discovery_rate(p_values)
np.testing.assert_allclose(corrected, fdr_fixed)
corrected = false_discovery_rate(p_values, m=len(p_values))
np.testing.assert_allclose(corrected, fdr_fixed)
corrected = false_discovery_rate(sorted(p_values), ordered=True)
np.testing.assert_allclose(sorted(corrected), sorted(fdr_fixed))
np.testing.assert_equal(false_discovery_rate([]), [])
np.testing.assert_equal(false_discovery_rate(p_values, m=-1), [])
dependant = [3.3414007065721947, 3.2688034599191167, 3.3480141985890031, 2.446462966857704,
3.2688034599191167, 3.3414007065721947, 3.4466345915436469, 3.2688034599191167,
3.4466345915436469, 3.2688034599191167, 3.2688034599191167, 3.2688034599191167,
2.554395156572014, 3.2688034599191167, 3.2688034599191167, 3.2688034599191167,
3.2688034599191167, 3.4466345915436469, 3.2688034599191167, 3.2688034599191167]
np.testing.assert_equal(false_discovery_rate(p_values, dependent=True), dependant)
def test_false_discovery_rate(self):
p_values = np.array([
0.727, 0.281, 0.791, 0.034, 0.628, 0.743, 0.958, 0.552, 0.867,
0.606, 0.611, 0.594, 0.071, 0.517, 0.526, 0.526, 0.635, 0.932,
0.210, 0.636
])
# calculated with http://www.sdmproject.com/utilities/?show=FDR
fdr_fixed = np.array([
0.92875, 0.9085714, 0.9305882, 0.68, 0.9085714, 0.92875, 0.958,
0.9085714, 0.958, 0.9085714, 0.9085714, 0.9085714, 0.71, 0.9085714,
0.9085714, 0.9085714, 0.9085714, 0.958, 0.9085714, 0.9085714
])
corrected = false_discovery_rate(p_values)
np.testing.assert_allclose(corrected, fdr_fixed)
corrected = false_discovery_rate(p_values, m=len(p_values))
np.testing.assert_allclose(corrected, fdr_fixed)
corrected = false_discovery_rate(sorted(p_values), ordered=True)
np.testing.assert_allclose(sorted(corrected), sorted(fdr_fixed))
np.testing.assert_equal(false_discovery_rate([]), [])
np.testing.assert_equal(false_discovery_rate(p_values, m=-1), [])
dependant = [
3.3414007065721947, 3.2688034599191167, 3.3480141985890031,
2.446462966857704, 3.2688034599191167, 3.3414007065721947,
3.4466345915436469, 3.2688034599191167, 3.4466345915436469,
3.2688034599191167, 3.2688034599191167, 3.2688034599191167,
2.554395156572014, 3.2688034599191167, 3.2688034599191167,
3.2688034599191167, 3.2688034599191167, 3.4466345915436469,
3.2688034599191167, 3.2688034599191167
]
np.testing.assert_equal(false_discovery_rate(p_values, dependent=True),
dependant)
def apply(self):
self.clear()
self.progressBarInit()
self.filter_enabled(False)
self.words = [i.name for i in self.selected_data_transformed.domain.attributes]
self.p_values = hypergeom_p_values(self.data.X,
self.selected_data_transformed.X,
callback=self.progress)
self.fdr_values = false_discovery_rate(self.p_values)
self.filter_and_display()
self.filter_enabled(True)
self.progressBarFinished()