Garfield.analysis.aggregate_top_markers

Garfield.analysis.aggregate_top_markers(ad, mks, groupby, n_genes=100, use_raw=True, **kwargs)[source]

Aggregate top marker genes.

Parameters:

  • ad (AnnData) – AnnData object containing expression data.

  • mks (DataFrame) – DataFrame containing marker statistics.

  • groupby (str) – Column in ad.obs used for grouping cells.

  • n_genes (int, optional) – Number of top genes to include in the test. Default is 100.

  • use_raw (bool, optional) – Whether to use raw expression values for the test. Default is True.

  • **kwargs (dict) – Additional keyword arguments passed to the rank_genes_groups function.

Returns:

Merged DataFrame with marker statistics and differential expression results.

Return type:

DataFrame