MiRTarBase

class openomics.database.interaction.MiRTarBase(path='http://mirtarbase.mbc.nctu.edu.tw/cache/download/7.0/', file_resources=None, source_col_name='miRNA', target_col_name='Target Gene', source_index='transcript_name', target_index='gene_name', edge_attr=None, filters={'Species (Target Gene)': 'Homo sapiens'}, directed=True, relabel_nodes=None, strip_mirna_name=False)

Bases: openomics.database.interaction.Interactions

Methods Summary

load_network(file_resources, …)

Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph.

Methods Documentation

load_network(file_resources, source_col_name, target_col_name, edge_attr, directed, filters)

Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph. :param file_resources: a dict of file name and file path/object :param source_col_name: column name of the dataframe for source in the edge :type source_col_name: str :param target_col_name: column name of the dataframe for target in the edge :type target_col_name: str :param edge_attr: list of str for column data to include in each edge :type edge_attr: list :param directed: True to return a DiGraph(), else Graph() :type directed: bool :param filters: A dict of {column name: column values} to filter the dataframe

Returns

a NetworkX Graph or DiGraph

Return type

network