cellink.tl.external.run_scprs_pipeline

cellink.tl.external.run_scprs_pipeline(adata, labels, gwas_file, prefix, prs_dir, cell_type_col=None, n_epoch=350, n_repeats=100, layer=3, l1=0.0, l2=0.0, lgraph=0.0, device='cuda:0', p_thresholds=None, r2_thresholds=None, knn_n_neighbors=25, n_pcs_knn=20, top_percentile=85.0, fdr_threshold=0.1, overwrite=False, save_model=False)

End-to-end scPRS pipeline.

Chains prepare_scprs_data() → run_scprs() → get_disease_relevant_cells().

Return type:

tuple

Returns:

tuple (weights_df, cell_results) if cell_type_col is None, (weights_df, cell_results, ct_results) otherwise.