tirank.Visualization.DEG_analysis

tirank.Visualization.DEG_analysis(savePath, fc_threshold=2, Pvalue_threshold=0.05, do_p_adjust=True)[source]

Performs and saves Differential Gene Expression (DEG) analysis.

This function loads a finalized AnnData object, computes DEGs between ‘Rank+’ and ‘Rank-’ groups using ‘wilcoxon’, saves all results, and then saves a filtered list of DEGs based on log-fold-change and p-value thresholds.

Parameters:

  • savePath (str) – The base directory containing the ‘3_Analysis’ subfolder, where ‘final_anndata.h5ad’ is located and results will be saved.

  • fc_threshold (float, optional) – The fold-change threshold for filtering. Defaults to 2.

  • Pvalue_threshold (float, optional) – The p-value threshold for filtering. Defaults to 0.05.

  • do_p_adjust (bool, optional) – If True, use adjusted p-values for filtering. If False, use raw p-values. Defaults to True.

Returns:

None