sccoda.util.data_generation.generate_case_control

sccoda.util.data_generation.generate_case_control(cases=1, K=5, n_total=1000, n_samples=[5, 5], sigma=None, b_true=None, w_true=None)

Generates compositional data with binary covariates.

Parameters

cases : intint (default: 1)

number of covariates. This will lead to D=2**cases columns in X, one for each combination of active/inactive covariates.

K : intint (default: 5)

Number of cell types

n_total : intint (default: 1000)

number of cells per sample

n_samples : List[any]List[any] (default: [5, 5])

Number of samples per case combination. len(n_samples)=[2**cases]

sigma : ndarray, NoneOptional[ndarray] (default: None)

correlation matrix for cell types,size KxK

b_true : ndarray, NoneOptional[ndarray] (default: None)

bias coefficients, size K

w_true : ndarray, NoneOptional[ndarray] (default: None)

Effect matrix, size DxK

Return type

AnnDataAnnData

Returns

• compositional data

• data – Anndata object