medusa.flux_analysis.deletion

Module Contents

medusa.flux_analysis.deletion.ensemble_single_reaction_deletion(ensemble, num_models=None, specific_models=[])

Performs single reaction deletions on models within an ensemble and returns the objective value after optimization with each reaction removed.

Parameters:

• ensemble (medusa.core.Ensemble) – The ensemble with which to perform reaction deletions
• num_models (int, optional) – Number of models for which reaction deletions will be performed. The number of models indicated will be randomly sampled and reaction deletions will be performed on the sampled models. If None, all models will be selected (default), or the models specified by specific_models will be selected. Cannot be passed concurrently with specific_models.
• specific_models (list of str, optional) – List of member.id corresponding to the models for which reaction deletions will be performed. If None, all models will be selected (default), or num_models will be randomly sampled and selected. Cannot be passed concurrently with num_models.

Returns:

A dataframe in which each row (index) represents a model within the ensemble, and each column represents a reaction for which values of objective when the reaction is deleted are returned.

Return type:

pandas.DataFrame

medusa.flux_analysis.deletion.ensemble_single_gene_deletion(ensemble, num_models=None, specific_models=[], specific_genes=[])

Performs single reaction deletions on models within an ensemble and returns the objective value after optimization with each reaction removed.

Parameters:

• ensemble (medusa.core.Ensemble) – The ensemble with which to perform reaction deletions
• num_models (int, optional) – Number of models for which reaction deletions will be performed. The number of models indicated will be randomly sampled and reaction deletions will be performed on the sampled models. If None, all models will be selected (default), or the models specified by specific_models will be selected. Cannot be passed concurrently with specific_models.
• specific_models (list of str, optional) – List of member.id corresponding to the models for which reaction deletions will be performed. If None, all models will be selected (default), or num_models will be randomly sampled and selected. Cannot be passed concurrently with num_models.
• specific_genes (list of str, optionsl) – List of gene.id corresponding to the genes for which deletions should be performed. If none, all genes will be selected (default). We recommend identifying genes that are essential in all ensemble members first, then excluding those genes from specific_genes. This will generally speed up computation.

Returns:

A dataframe in which each row (index) represents a model within the ensemble, and each column represents a reaction for which values of objective when the reaction is deleted are returned.

Return type:

pandas.DataFrame