LncBase#

class openomics.database.interaction.LncBase(path='https://dianalab.e-ce.uth.gr/downloads/', file_resources=None, strip_mirna_name=False, source_col_name='mirna', target_col_name='geneId', edge_attr=None, filters=None, directed=True, relabel_nodes=None)[source][source]#

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

Loads the LncBase database from http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex .

Default path: local_directory . Default file_resources: {

“LncBasev2_download.csv”: “LncBasev2_download.csv””,

}

Methods Summary

`get_rename_dict`([from_index, to_index])
`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

get_rename_dict(from_index='geneId', to_index='geneName')[source][source]#

load_network(file_resources, source_col_name, target_col_name, edge_attr, directed, filters, blocksize=None)[source][source]#

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