decoupler.run_aucell
- decoupler.run_aucell(mat, net, source='source', target='target', n_up=None, min_n=5, seed=42, verbose=False, use_raw=True)
AUCell.
Wrapper to run AUCell.
- Parameters:
- matlist, pd.DataFrame or AnnData
List of [features, matrix], dataframe (samples x features) or an AnnData instance.
- netpd.DataFrame
Network in long format.
- sourcestr
Column name in net with source nodes.
- targetstr
Column name in net with target nodes.
- n_upint
Number of top ranked features to select as observed features. If not specified it will be equal to the 5% of the number of features.
- min_nint
Minimum of targets per source. If less, sources are removed.
- seedint
Random seed to use.
- verbosebool
Whether to show progress.
- use_rawbool
Use raw attribute of mat if present.
- Returns:
- Returns aucell activity estimates or stores them in mat.obsm[‘aucell_estimate’].