decoupler.get_gsea_df
- decoupler.get_gsea_df(df, stat, net, source='source', target='target', times=1000, min_n=5, seed=42, verbose=False)
Wrapper to run GSEA for results of differential analysis (long format dataframe).
- Parameters:
- dfDataFrame
Long format DataFrame with features to be ranked. Assumes features are indexes.
- statstr
Name of the column containing the ranking metric.
- netDataFrame
Network in long format.
- sourcestr
Column name in net with source nodes.
- targetstr
Column name in net with target nodes.
- timesint
How many random permutations to do.
- min_nint
Minimum of targets per source. If less, sources are removed.
- seedint
Random seed to use.
- verbosebool
Whether to show progress.
- Returns:
- resultsDataFrame
Results of GSEA.