decoupler.run_ora
- decoupler.run_ora(mat, net, source='source', target='target', n_up=None, n_bottom=0, n_background=20000, min_n=5, seed=42, verbose=False, use_raw=True)
Over Representation Analysis (ORA).
Wrapper to run ORA.
- 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.
- n_bottomint
Number of bottom ranked features to select as observed features.
- n_backgroundint
Integer indicating the background size.
- 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 ora activity estimates (-log10(p-values)) and p-values
- or stores them in mat.obsm[‘ora_estimate’] and
- mat.obsm[‘ora_pvals’].