14.1.6. cobra.topology package¶
14.1.6.1. Submodules¶
14.1.6.2. cobra.topology.reporter_metabolites module¶
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cobra.topology.reporter_metabolites.identify_reporter_metabolites(cobra_model, reaction_scores_dict, number_of_randomizations=1000, scoring_metric='default', score_type='p', entire_network=False, background_correction=True, ignore_external_boundary_reactions=False)[source]¶ Calculate the aggregate Z-score for the metabolites in the model. Ignore reactions that are solely spontaneous or orphan. Allow the scores to have multiple columns / experiments. This will change the way the output is represented.
cobra_model: A cobra.Model object
TODO: CHANGE TO USING DICTIONARIES for the_reactions: the_scores
reaction_scores_dict: A dictionary where the keys are reactions in cobra_model.reactions and the values are the scores. Currently, only supports a single numeric value as the value; however, this will be updated to allow for lists
number_of_randomizations: Integer. Number of random shuffles of the scores to assess which are significant.
scoring_metric: default means divide by k**0.5
score_type: ‘p’ Is the only option at the moment and indicates p-value.
entire_network: Boolean. Currently, only compares scores calculated from the_reactions
background_correction: Boolean. If True apply background correction to the aggreagate Z-score
ignore_external_boundary_reactions: Not yet implemented. Boolean. If True do not count exchange reactions when calculating the score.