harreman.tools.select_significant_interactions

harreman.tools.select_significant_interactions(adata, ct_aware=False, test='parametric', use_FDR=True, threshold=0.05)

Select significant gene pairs or metabolite-mediated interactions based on FDR/p-value thresholds and (optionally) cell-type–aware tests.

Parameters:

• adata (AnnData) –

  AnnData object containing: - uns['ccc_results'] or uns['ct_ccc_results'], each of which includes:

  • cell_com_df_gp: DataFrame with statistics for gene pairs

  • cell_com_df_m: DataFrame with statistics for metabolites

• ct_aware (bool, default False) – If True, use cell-type–aware CCC results (uns['ct_ccc_results']). If False, use cell-type-agnostic CCC results (uns['ccc_results']).

• test ({"parametric", "non-parametric"}, default "parametric") – Determines which statistical columns to use: - Parametric: Z_FDR / Z_pval, C_p - Non-parametric: FDR_np / pval_np, C_np

• use_FDR (bool, default True) – If True, threshold significance using FDR values. If False, use raw p-values.

• threshold (float, default 0.05) – Significance cutoff applied to the selected statistic (FDR or p-value).