spamosaic.preprocessing.Epigenome_preprocess

spamosaic.preprocessing.Epigenome_preprocess(epi_ads, batch_corr=False, n_peak=100000, n_comps=50, batch_key='src', key='dimred_bc', return_hvf=False)[source]

Preprocessing pipeline for epigenomic modality (e.g. ATAC-seq).

Parameters:

  • epi_ads (list of AnnData) – Epigenomic modality per batch.

  • batch_corr (bool) – Whether to apply Harmony batch correction.

  • n_peak (int) – Number of variable peaks to keep.

  • n_comps (int) – Number of LSI components.

  • batch_key (str) – Batch identifier key.

  • key (str) – Output key in .obsm.

  • return_hvf (bool) – Whether to return selected peak indices.

Returns:

If return_hvf is True, returns names and indices of selected peaks.

Return type:

Optional[Tuple[np.ndarray, np.ndarray]]