zoom.sc_tool.downstream_DEG

zoom.sc_tool.downstream_DEG(adata: anndata.AnnData, df_res: pandas.DataFrame, alpha: float, min_score: float, group: str, rank_method: str, max_iter: int) → anndata.AnnData[source]

Calculates differentially expressed genes (DEG) for cell groups containing cells significantly relevant to SBP.

Parameters:

  • adata (ad.AnnData) – The AnnData object containing expression data. - adata.X should have underwent gene specificity score normalization.

  • df_res (pd.DataFrame) – Results of single-cell SBP-relevant enrichment scores and other statistics.

  • alpha (float) – Significance level indicating significant cell subpopulations.

  • min_score (float) – Minimum enrichment score for significant cell subpopulations.

  • group (str) – Column name indicating the cell groups, based on which significant cells and non-significant cells are compared, must be present in adata.obs.

  • rank_method ({'t-test','t-test_overestim_var','wilcoxon','logreg'}) – Methods how scanpy calculate differentially expressed genes.

  • max_iter (int) – Maximum iteration for DEG calculation, only used for logreg.

Returns:

adata – The AnnData object with adata.uns[‘DEG’], where the DEG results for each cell group are stored.

Return type:

ad.AnnData