Garfield.preprocessing.preprocessing_atac

Garfield.preprocessing.preprocessing_atac(adata: AnnData, used_hvgs: bool = True, used_lsi_norm: bool = False, used_lsi_graph: bool = True, min_features: int = 100, min_cells: int = 3, atac_n_top_features=100000, n: int = 6, batch_key: str = 'batch', metric: str = 'euclidean', n_components: int = 50)

Preprocess scATAC data matrix.

Parameters:

• adata (AnnData object of shape n_obs × n_vars. Rows correspond to cells and columns to peaks/regions.)

• filter_rate (float, optional) – Proportion for feature selection, by default 0.01