thor.analy.compute_dge_between_regions

thor.analy.compute_dge_between_regions(ad_r1: AnnData, ad_r2: AnnData, test_method: str = 't-test', pval_cutoff: float = 0.01, log2fc_min: float = 1, log2fc_max: float | None = None) → DataFrame

Compute differential gene expression (DGE) between two regions.

Parameters:

  • ad_r1 (AnnData) – Annotated data matrix for region 1.

  • ad_r2 (AnnData) – Annotated data matrix for region 2.

  • test_method (str, optional) – Statistical test method to use for DGE analysis. Valid options are ‘logreg’, ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’. Default is ‘t-test’.

  • pval_cutoff (float, optional) – P-value cutoff for significance, by default 0.01.

  • log2fc_min (float, optional) – Minimum log2 fold change for significance, by default 1.

  • log2fc_max (float, optional) – Maximum log2 fold change for significance, by default None.

Returns:

A numpy array containing the DGE results.

Return type:

np.ndarray