neko.core.network.Network.connect_genes_to_phenotype

Network.connect_genes_to_phenotype(phenotype: str | None = None, id_accession: str | None = None, sub_genes: list[str] | None = None, maxlen: int = 2, only_signed: bool = False, compress: bool = False) → None

This function connects genes to a phenotype based on the provided Args. It retrieves phenotype markers, identifies unique Uniprot genes, and connects them to the network. It also has the option to compress the network by substituting specified genes with the phenotype name.

Args:

• phenotype: The phenotype to connect to. If not provided, it will be retrieved using the id_accession.

• id_accession: The accession id of the phenotype. If not provided, the phenotype parameter must be given.

• sub_genes: A list of genes to be considered for connection. If not provided, all nodes in the network are

  considered.

• maxlen: The maximum length of the paths to be searched for.

• only_signed: A boolean flag to indicate whether to filter unsigned paths.

• compress: A boolean flag to indicate whether to substitute the specified genes with the phenotype name.

Returns:

• None