get_regulatory_network {regutools} | R Documentation |
This function retrieves all the regulation networks in regulonDB between TF-TF, GENE-GENE or TF-GENE depending on the parameter 'type'.
get_regulatory_network( regulondb, regulator = NULL, type = "TF-GENE", cytograph = FALSE )
regulondb |
A |
regulator |
Name of TF or gene that acts as regulator. If |
type |
"TF-GENE", "TF-TF", "GENE-GENE" |
cytograph |
If TRUE, displays network in Cytoscape. This option requires previous instalation and launch of Cytoscape. |
A regulondb_result object.
Carmina Barberena Jonas, Jesús Emiliano Sotelo Fonseca, José Alquicira Hernández, Joselyn Chávez
## Connect to the RegulonDB database if necessary if (!exists("regulondb_conn")) regulondb_conn <- connect_database() ## Build the regulon db object e_coli_regulondb <- regulondb( database_conn = regulondb_conn, organism = "E.coli", database_version = "1", genome_version = "1" ) ## Retrieve regulation of 'araC' get_regulatory_network(e_coli_regulondb, regulator = "AraC", type = "TF-GENE" ) ## Retrieve all GENE-GENE networks get_regulatory_network(e_coli_regulondb, type = "GENE-GENE") ## Retrieve TF-GENE network of AraC and display in Cytoscape ## Note that Cytospace needs to be open for this to work cytoscape_present <- try(RCy3::cytoscapePing(), silent = TRUE) if (!is(cytoscape_present, "try-error")) { get_regulatory_network( e_coli_regulondb, regulator = "AraC", type = "TF-GENE", cytograph = TRUE ) }