TarBase

class openomics.database.interaction.TarBase(path='https://dianalab.e-ce.uth.gr/downloads', file_resources=None, source_col_name='mirna', target_col_name='geneName', edge_attr=None, filters=None, directed=True, relabel_nodes=None, blocksize=None, **kwargs)

Bases: openomics.database.interaction.Interactions

Methods Summary

load_dataframe(file_resources[, blocksize])	Handles data preprocessing given the file_resources input, and returns a DataFrame.
load_network(file_resources, ...[, blocksize])	Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph.

Methods Documentation

load_dataframe(file_resources, blocksize=None)

Handles data preprocessing given the file_resources input, and returns a DataFrame.

Parameters

• file_resources (dict) – A dict with keys as filenames and values as full file path.

• blocksize (int) –

Return type

DataFrame

load_network(file_resources, source_col_name, target_col_name, edge_attr, directed, filters, blocksize=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 :param blocksize ():

Returns

a NetworkX Graph or DiGraph

Return type

network