def test_heritability(self):
snp_data, pheno, covar, X, Y, K = util.load_data(os.path.dirname(os.path.realpath(__file__))+"/sim_data", os.path.dirname(os.path.realpath(__file__))+"/sim_data.pheno", None)
y_pheno, m, _, estimated_h2 = warped_stepwise(Y, X, K, covariates=covar,
max_covariates=10,
num_restarts=1,
qv_cutoff=0.05,
pv_cutoff=None)
print estimated_h2
self.assertTrue(np.allclose(estimated_h2, 0.5, atol=5e-2))
def test_heritability(self):
snp_data, pheno, covar, X, Y, K = util.load_data(
os.path.dirname(os.path.realpath(__file__)) + "/sim_data",
os.path.dirname(os.path.realpath(__file__)) + "/sim_data.pheno",
None)
y_pheno, m, _, estimated_h2 = warped_stepwise(Y,
X,
K,
covariates=covar,
max_covariates=10,
num_restarts=1,
qv_cutoff=0.05,
pv_cutoff=None)
print estimated_h2
self.assertTrue(np.allclose(estimated_h2, 0.5, atol=5e-2))
def test_load(self):
snp_data, pheno, covar, X, Y, K = util.load_data(
os.path.dirname(os.path.realpath(__file__)) + "/sim_data",
os.path.dirname(os.path.realpath(__file__)) + "/sim_data.pheno",
None)
def test_load(self):
snp_data, pheno, covar, X, Y, K = util.load_data(os.path.dirname(os.path.realpath(__file__))+"/sim_data", os.path.dirname(os.path.realpath(__file__))+"/sim_data.pheno", None)
