decoupler.get_ora_df
- decoupler.get_ora_df(df, net, groupby, features, source='source', target='target', n_background=20000, min_n=5, verbose=False)
Wrapper to run ORA without an input matrix, instead it uses an input DataFrame in long format with one group columns and the significant features in another. Useful for results of differential analysis where no mat is available.
- Parameters:
- dfDataFrame
Long format DataFrame with groups and significant features.
- netDataFrame
Network in long format.
- groupbystr
Column name in df with groups.
- featuresstr
Column name in df with significant features.
- sourcestr
Column name in net with source nodes.
- targetstr
Column name in net with target nodes.
- n_backgroundint
Integer indicating the background size.
- min_nint
Minimum of targets per source. If less, sources are removed.
- verbosebool
Whether to show progress.
- Returns:
- pvalsDataFrame
Obtained p-values per group and source.