from obnb.data.network.base import BaseNDExData
from obnb.typing import Converter
[docs]class FunCoup(BaseNDExData):
"""The FunCoup funcional association network.
The edge weights are PFC values, which is a probabilistic estimation about
whether a pair of genes are functionally coupled.
https://funcoup5.scilifelab.se/help/#Citation
"""
cx_uuid = "172990f7-102f-11ec-b666-0ac135e8bacf"
def __init__(
self,
root: str,
*,
weighted: bool = True,
directed: bool = False,
largest_comp: bool = True,
gene_id_converter: Converter = "HumanEntrez",
**kwargs,
):
"""Initialize the FunCoup network data."""
super().__init__(
root,
weighted=True,
directed=False,
largest_comp=True,
gene_id_converter="HumanEntrez",
cx_kwargs={
"interaction_types": ["has functional association with"],
"node_id_prefix": "ensembl",
"default_edge_weight": 0.0,
"edge_weight_attr_name": "#0:PFC",
"reduction": "max",
},
**kwargs,
)