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)
