epiaster.ensemble.estimate_k

epiaster.ensemble.estimate_k(adata, search_list, binary=True, fpeak=0.01, seed=2022)

Estimate the number of cell types in scCAS data by ASTER.

Parameters

• adata – AnnData object of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

• search_list – List of optional numbers of cell types for the estimation.

• binary – Whether to convert the count matrix into a binary matrix. By default, binary=True.

• fpeak – Select peaks/regions that have at least one read count in at least fpeak of the cells in the count matrix. By default, fpeak=0.01.

• seed – Random seed for reproducibility. By default, seed=None.

Returns

Estimated number of cell types.

Return type

estimated_k