gcell.cell.celltype.GETHydraCellType.get_tf_pathway#
- GETHydraCellType.get_tf_pathway(tf, gp=None, quantile_cutoff=0.9, exp_cutoff=0, filter_str='term_size<1000 & term_size>500', significance_threshold_method='g_SCS')[source]#
This function retrieves the pathway for a given transcription factor (tf) using g:Profiler.
- Parameters:
- tf
The transcription factor to get the pathway for.
- gp default:
None An instance of the GProfiler class. If None, a new instance will be created. Defaults to None.
- quantile_cutoff default:
0.9 The quantile cutoff to use when selecting genes. Defaults to 0.9.
- exp_cutoff default:
0 The expression cutoff to use when querying genes. Defaults to 0.
- filter_str default:
'term_size<1000 & term_size>500' The filter string to use when querying the g:Profiler results. Defaults to ‘term_size<1000 & term_size>500’.
- significance_threshold_method default:
'g_SCS' The method to use for determining the significance threshold in g:Profiler. Defaults to ‘g_SCS’.
- Returns:
tuple: A tuple containing the filtered g:Profiler results and the unique genes in the pathways.