Utils¶
This module contains miscellaneous methods.
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compath.utils.
dict_to_pandas_df
(d)[source]¶ Transform pandas df into a dict.
- Parameters
d (dict) –
- Return type
pandas.DataFrame
- Returns
pandas dataframe
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compath.utils.
process_form_gene_set
(text)[source]¶ Process the string containing gene symbols and returns a gene set.
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compath.utils.
calculate_relative_enrichments
(results, total_pathways_by_resource)[source]¶ Calculate relative enrichment of pathways (enriched pathways/total pathways).
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compath.utils.
count_genes_in_pathway
(pathways_gene_sets, genes)[source]¶ Calculate how many of the genes are associated to each pathway gene set.
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compath.utils.
simulate_pathway_enrichment
(resource_gene_sets, gene_set_query, runs=200)[source]¶ Simulate pathway enrichment.
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compath.utils.
get_genes_without_assigned_pathways
(enrichment_results, genes_query)[source]¶ Return the genes without any known pathway assigned.
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compath.utils.
get_enriched_pathways
(manager_list, gene_set)[source]¶ Return the results of the queries for every registered manager.
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compath.utils.
get_gene_pathways
(manager_list, gene)[source]¶ Return the pathways associated with a gene for every registered manager.
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compath.utils.
get_mappings
(compath_manager, only_accepted=True)[source]¶ Return a pandas dataframe with mappings information as an excel sheet file.
- Parameters
compath_manager (compath.manager.Manager) – ComPath Manager
only_accepted (bool) – only accepted (True) or all (False)
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compath.utils.
get_pathway_model_by_name
(manager_dict, resource, pathway_name)[source]¶ Return the pathway object from the resource manager.
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compath.utils.
get_pathway_model_by_id
(app, resource, pathway_id)[source]¶ Return the pathway object from the resource manager.
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compath.utils.
get_gene_sets_from_pathway_names
(app, pathways)[source]¶ Return the gene sets for a given pathway/resource tuple.
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compath.utils.
get_pathway_info
(app, pathways)[source]¶ Return the gene sets for a given pathway/resource tuple.
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compath.utils.
get_last_action_in_module
(module_name, action)[source]¶ Return the info about the last action in the given module.
- Parameters
module_name (str) –
- Returns
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compath.utils.
perform_hypergeometric_test
(gene_set, manager_pathways_dict, gene_universe, apply_threshold=False, threshold=0.05)[source]¶ Perform hypergeometric tests.
- Parameters
- Return type
- Returns
manager_pathways_dict with p value info
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compath.utils.
calculate_szymkiewicz_simpson_coefficient
(set_1, set_2)[source]¶ Calculate Szymkiewicz-Simpson coefficient between two sets.
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compath.utils.
calculate_similarity
(name_1, name_2)[source]¶ Calculate the string based similarity between two names.
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compath.utils.
get_top_matches
(matches, top)[source]¶ Order list of tuples by second value and returns top values.
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compath.utils.
filter_results
(results, threshold)[source]¶ Filter a tuple based iterator given a threshold.