def testBasicWithCovar(self):
PhenoCovar.sex_as_covariate = False
pc = PhenoCovar()
load_pedigree(pc, self.ped)
pc.individual_mask = [0, 0, 0, 0, 0, 0, 1, 1]
pc.load_covarfile(self.header, names=["BMI", "MSA"])
pc.freeze_subjects()
pheno = [0.1, 0.4, 1.0, 0.5, 0.9, 1.0]
sex = [1, 1, 2, 1, 1, 1]
# First, test without sex as covariate
count = 0
for test in pc:
test_pheno, covars, nonmissing = test.get_variables()
self.assertEqual(6, numpy.sum(nonmissing))
self.assertEqual(2, len(covars))
for phenotype in self.phenotypes[0:2]:
self.assertEqual(self.phenotypes[0], list(covars[0]))
self.assertEqual(self.phenotypes[2], list(covars[1]))
self.assertEqual("BMI", test.get_covariate_name(0))
self.assertEqual("MSA", test.get_covariate_name(1))
self.assertEqual(6, len(pheno))
self.assertEqual("Pheno-1", test.get_phenotype_name())
for i in range(0, len(pheno)):
self.assertAlmostEqual(pheno[i], test_pheno[i])
count += 1
self.assertEqual(1, count)
PhenoCovar.sex_as_covariate = True
def testBasicWithMask(self):
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
load_pedigree(pc, self.ped)
pc.individual_mask = [0, 0, 1, 0, 0, 0, 1, 0]
orig_pheno = [0.1, 0.4, 0.5, 0.9, 1.0, 0.9]
sex = [1, 1, 2, 1, 1, 1]
count = 0
for test in pc:
pheno, covars, nonmissing = test.get_variables(numpy.array(pc.individual_mask, dtype=bool))
self.assertEqual(6, numpy.sum(nonmissing))
self.assertEqual(1, len(covars))
self.assertEqual(sex, list(covars[count]))
self.assertEqual("SEX", test.get_covariate_name(count))
self.assertEqual(6, len(pheno))
self.assertEqual("Pheno-1", test.get_phenotype_name())
for idx in range(0, len(pheno)):
self.assertEqual(orig_pheno[idx], pheno[idx])
count += 1
self.assertEqual(1, count)
