LncBase

class openomics.database.interaction.LncBase(path, file_resources=None, strip_mirna_name=False, source_col_name='mirna', target_col_name='geneId', source_index='transcript_name', target_index='gene_id', edge_attr=None, filters={'species': 'Homo sapiens'}, directed=True, relabel_nodes=None)

Bases: openomics.database.interaction.Interactions, openomics.database.base.Database

Methods Summary

get_rename_dict([from_index, to_index])
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

get_rename_dict(from_index='geneId', to_index='geneName')

load_network(file_resources, source_col_name='mirna', target_col_name='gene_id', edge_attr=None, directed=True, filters=None)

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