decoupler.run_viper
- decoupler.run_viper(mat, net, source='source', target='target', weight='weight', pleiotropy=True, reg_sign=0.05, n_targets=10, penalty=20, batch_size=10000, min_n=5, verbose=False, use_raw=True)
Virtual Inference of Protein-activity by Enriched Regulon (VIPER).
Wrapper to run VIPER.
- 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.
- weightstr
Column name in net with weights.
- pleiotropybool
Logical, whether correction for pleiotropic regulation should be performed.
- reg_signfloat
Pleiotropy argument. p-value threshold for considering significant regulators.
- n_targetsint
Pleiotropy argument. Integer indicating the minimal number of overlaping targets to consider for analysis.
- penaltyint
Number higher than 1 indicating the penalty for the pleiotropic interactions. 1 = no penalty.
- batch_sizeint
Size of the batches to use. Increasing this will consume more memmory but it will run faster.
- min_nint
Minimum of targets per source. If less, sources are removed.
- verbosebool
Whether to show progress.
- use_rawbool
Use raw attribute of mat if present.
- Returns:
- Returns viper activity estimates and p-values or stores them in mat.obsm[‘viper_estimate’] and mat.obsm[‘viper_pvals’].