def testAgainstQValue(self):
R.assign("pvalues", self.pvalues)
qvalue = R('''qvalue( pvalues )''')
r_qvalues = qvalue[2]
r_pi0 = qvalue[1][0]
new = Stats.doFDRPython(self.pvalues)
self.assertTrue(getRelativeError(r_pi0, new.mPi0) < self.max_error)
for a, b in zip(r_qvalues, new.mQValues):
self.assertAlmostEqual(a, b, places=self.nplaces)
def testAgainstQValue(self):
R.assign("pvalues", self.pvalues)
qvalue = R('''qvalue( pvalues )''')
r_qvalues = qvalue[2]
r_pi0 = qvalue[1][0]
new = Stats.doFDRPython(self.pvalues)
self.assertTrue(getRelativeError(r_pi0, new.mPi0) < self.max_error)
for a, b in zip(r_qvalues, new.mQValues):
self.assertAlmostEqual(a, b, places=self.nplaces)
def checkFDR(self, **kwargs):
old = Stats.doFDR(self.pvalues, **kwargs)
# print old.mQValues[:10]
# print old.mPi0
new = Stats.doFDRPython(self.pvalues, **kwargs)
# print new.mQValues[:10]
# print new.mPi0
# self.assertAlmostEqual( old.mPi0, new.mPi0, places=3)
self.assertTrue(getRelativeError(old.mPi0, new.mPi0) < self.max_error)
for pvalue, a, b in zip(self.pvalues, old.mQValues, new.mQValues):
self.assertTrue(
getRelativeError(a, b) < self.max_error,
"qvalues: relative error %f > %f (pvalue=%f, %f, %f)" %
(getRelativeError(a, b), self.max_error, pvalue, a, b))
def checkFDR(self, **kwargs):
old = Stats.doFDR(self.pvalues, **kwargs)
# print old.mQValues[:10]
# print old.mPi0
new = Stats.doFDRPython(self.pvalues, **kwargs)
# print new.mQValues[:10]
# print new.mPi0
# self.assertAlmostEqual( old.mPi0, new.mPi0, places=3)
self.assertTrue(getRelativeError(old.mPi0, new.mPi0) < self.max_error)
for pvalue, a, b in zip(self.pvalues, old.mQValues, new.mQValues):
self.assertTrue(getRelativeError(a, b) < self.max_error,
"qvalues: relative error %f > %f (pvalue=%f, %f, %f)" %
(getRelativeError(a, b),
self.max_error,
pvalue, a, b))
