def setUp(self): sample_nums = range(1, 13) colnames = ["gene_id"] + ["sample" + str(x) for x in sample_nums] roles = ['feature_id'] for i in range(len(sample_nums)): roles.append('sample') schema = Schema(column_names=colnames, column_roles=roles) schema.add_factor('age', [2, 20, 55]) schema.add_factor('sex', ['male', 'female']) schema.add_factor('treated', [False, True]) counter = 0 self.assertEquals(schema.sample_num("sample1"), 0) self.assertEquals(schema.sample_num("sample7"), 6) for sex in ['male', 'female']: for age in [2, 20, 55]: for treated in [True, False]: counter += 1 name = "sample" + str(counter) schema.set_factor(name, 'sex', sex) schema.set_factor(name, 'age', age) schema.set_factor(name, 'treated', treated) self.schema = schema
def setUp(self): sample_nums = range(1, 13) colnames = ["gene_id"] + ["sample" + str(x) for x in sample_nums] roles = ['feature_id'] for i in range(len(sample_nums)): roles.append('sample') schema = Schema( column_names=colnames, column_roles=roles) schema.add_factor('age', [2, 20, 55]) schema.add_factor('sex', ['male', 'female']) schema.add_factor('treated', [False, True]) counter = 0 self.assertEquals(schema.sample_num("sample1"), 0); self.assertEquals(schema.sample_num("sample7"), 6); for sex in ['male', 'female']: for age in [2, 20, 55]: for treated in [True, False]: counter += 1 name = "sample" + str(counter) schema.set_factor(name, 'sex', sex) schema.set_factor(name, 'age', age) schema.set_factor(name, 'treated', treated) self.schema = schema
def test_model_dummy_vars_1(self): sample_nums = range(1, 13) colnames = ["gene_id"] + ["sample" + str(x) for x in sample_nums] roles = ['feature_id'] for i in range(len(sample_nums)): roles.append('sample') schema = Schema( column_names=colnames, column_roles=roles) schema.add_factor('age', [2, 20, 55]) schema.add_factor('sex', ['male', 'female']) schema.add_factor('treated', [False, True]) counter = 0 self.assertEquals(schema.sample_num("sample1"), 0); self.assertEquals(schema.sample_num("sample7"), 6); for sex in ['male', 'female']: for age in [2, 20, 55]: for treated in [True, False]: counter += 1 name = "sample" + str(counter) schema.set_factor(name, 'sex', sex) schema.set_factor(name, 'age', age) schema.set_factor(name, 'treated', treated) dummies = dummy_vars(schema, ['age', 'treated'], level=2) expected = DummyVarTable( ({}, {'age': 20}, {'age': 55}, {'treated': True}, {'age': 20, 'treated': True}, {'age': 55, 'treated': True}), [ DummyVarAssignment(factor_values=(2, False), bits=(True, False, False, False, False, False), indexes=['sample2', 'sample8']), DummyVarAssignment(factor_values=(2, True), bits=(True, False, False, True, False, False), indexes=['sample1', 'sample7']), DummyVarAssignment(factor_values=(20, False), bits=(True, True, False, False, False, False), indexes=['sample4', 'sample10']), DummyVarAssignment(factor_values=(20, True), bits=(True, True, False, True, True, False), indexes=['sample3', 'sample9']), DummyVarAssignment(factor_values=(55, False), bits=(True, False, True, False, False, False), indexes=['sample6', 'sample12']), DummyVarAssignment(factor_values=(55, True), bits=(True, False, True, True, False, True), indexes=['sample5', 'sample11'])]) self.assertEquals(dummies, expected)
def test_model_dummy_vars_1(self): sample_nums = range(1, 13) colnames = ["gene_id"] + ["sample" + str(x) for x in sample_nums] roles = ['feature_id'] for i in range(len(sample_nums)): roles.append('sample') schema = Schema(column_names=colnames, column_roles=roles) schema.add_factor('age', [2, 20, 55]) schema.add_factor('sex', ['male', 'female']) schema.add_factor('treated', [False, True]) counter = 0 self.assertEquals(schema.sample_num("sample1"), 0) self.assertEquals(schema.sample_num("sample7"), 6) for sex in ['male', 'female']: for age in [2, 20, 55]: for treated in [True, False]: counter += 1 name = "sample" + str(counter) schema.set_factor(name, 'sex', sex) schema.set_factor(name, 'age', age) schema.set_factor(name, 'treated', treated) dummies = dummy_vars(schema, ['age', 'treated'], level=2) expected = DummyVarTable(({}, { 'age': 20 }, { 'age': 55 }, { 'treated': True }, { 'age': 20, 'treated': True }, { 'age': 55, 'treated': True }), [ DummyVarAssignment(factor_values=(2, False), bits=(True, False, False, False, False, False), indexes=['sample2', 'sample8']), DummyVarAssignment(factor_values=(2, True), bits=(True, False, False, True, False, False), indexes=['sample1', 'sample7']), DummyVarAssignment(factor_values=(20, False), bits=(True, True, False, False, False, False), indexes=['sample4', 'sample10']), DummyVarAssignment(factor_values=(20, True), bits=(True, True, False, True, True, False), indexes=['sample3', 'sample9']), DummyVarAssignment(factor_values=(55, False), bits=(True, False, True, False, False, False), indexes=['sample6', 'sample12']), DummyVarAssignment(factor_values=(55, True), bits=(True, False, True, True, False, True), indexes=['sample5', 'sample11']) ]) self.assertEquals(dummies, expected)