spapros.se.select_DE_genes

spapros.se.select_DE_genes(adata, n, per_group=False, obs_key='celltype', penalty_keys=[], groups='all', reference='rest', rankby_abs=False, inplace=True, progress=None, verbosity=2, level=2, task='Select DE genes...')

Select genes based on wilxocon rank genes test.

Parameters:

  • adata (AnnData) – Data with log normalised counts in adata.X.

  • n (int) – int Number of genes to selected (in total if not per_group else per group).

  • per_group (bool) – Select n genes per group of adata.obs[obs_key] (default: False). Note that the same gene can be selected for multiple groups.

  • obs_key (str) – Column name of adata.obs for which marker scores are calculated.

  • penalty_keys (list) – Penalty factor for gene selection.

  • groups (Union[Literal['all'], ~typing.Iterable[str]]) – See sc.tl.rank_genes_groups().

  • reference (str) – See sc.tl.rank_genes_groups() but extended to lists of reference groups. Note that in case of providing such a list you need to include all elements of groups in reference.

  • rankby_abs (bool) – See sc.tl.rank_genes_groups().

  • inplace (bool) – Save results in adata.var or return dataframe.

  • progress (Optional[Progress]) – rich.Progress object if progress bars should be shown.

  • verbosity (int) – Verbosity level.

  • level (int) – Progress bar level.

  • task (str) – Description of progress task.

Returns:

Index are genes as in adata.var.index. It contains a bool column named ‘selection’.

Return type:

pd.DataFrame