def checkFDR(self, pi0_method):
result = Stats.doFDR(self.mPvalues,
fdr_level=0.05,
pi0_method=pi0_method)
R("""require ('qvalue')""")
qvalues = R.qvalue(ro.FloatVector(self.mPvalues),
fdr_level=0.05,
pi0_method=pi0_method)
assert qvalues.names[1] == "pi0"
assert qvalues.names[2] == "qvalues"
assert qvalues.names[5] == "significant"
assert qvalues.names[6] == "lambda"
r_qvalues = qvalues[2]
r_pi0 = qvalues[1][0]
self.assertEqual(len(result.mQValues), len(qvalues[2]))
self.assertEqual(len(result.mLambda), len(qvalues[6]))
self.assertEqual(result.mPi0, r_pi0)
for a, b in zip(result.mQValues, r_qvalues):
self.assertAlmostEqual(a, b, 2, "unequal: %f != %f" % (a, b))
for a, b in zip(result.mPassed, qvalues[5]):
self.assertEqual(
a, b, "threshold-passed flag not equal: %s != %s" % (a, b))
def checkFDR(self, pi0_method):
result = Stats.doFDR(
self.mPvalues, fdr_level=0.05, pi0_method=pi0_method)
R("""require ('qvalue')""")
qvalues = R.qvalue(ro.FloatVector(self.mPvalues),
fdr_level=0.05,
pi0_method=pi0_method)
assert qvalues.names[1] == "pi0"
assert qvalues.names[2] == "qvalues"
assert qvalues.names[5] == "significant"
assert qvalues.names[6] == "lambda"
r_qvalues = qvalues[2]
r_pi0 = qvalues[1][0]
self.assertEqual(len(result.mQValues), len(qvalues[2]))
self.assertEqual(len(result.mLambda), len(qvalues[6]))
self.assertEqual(result.mPi0, r_pi0)
for a, b in zip(result.mQValues, r_qvalues):
self.assertAlmostEqual(a, b, 2, "unequal: %f != %f" % (a, b))
for a, b in zip(result.mPassed, qvalues[5]):
self.assertEqual(
a, b, "threshold-passed flag not equal: %s != %s" % (a, b))
def q_value_analysis(p_values):
logging.info('q-value analysis on %d p-values', len(p_values))
from rpy2.robjects import r, FloatVector
r.library('qvalue')
ps = FloatVector(p_values)
qobj = r.qvalue(ps)
return qobj
def q_value_analysis(p_values):
logging.info("q-value analysis on %d p-values", len(p_values))
from rpy2.robjects import r, FloatVector
r.library("qvalue")
ps = FloatVector(p_values)
qobj = r.qvalue(ps)
return qobj
