get_regulatory_network: Return complete regulatory network.

Description Usage Arguments Value Author(s) Examples

View source: R/get_regulatory_network.R

Description

This function retrieves all the regulation networks in regulonDB between TF-TF, GENE-GENE or TF-GENE depending on the parameter 'type'.

Usage

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get_regulatory_network(
  regulondb,
  regulator = NULL,
  type = "TF-GENE",
  cytograph = FALSE
)

Arguments

regulondb

A regulondb() object.

regulator

Name of TF or gene that acts as regulator. If NULL, the function retrieves all existent networks in the regulonDB.

type

"TF-GENE", "TF-TF", "GENE-GENE"

cytograph

If TRUE, displays network in Cytoscape. This option requires previous instalation and launch of Cytoscape.

Value

A regulondb_result object.

Author(s)

Carmina Barberena Jonas, Jesús Emiliano Sotelo Fonseca, José Alquicira Hernández, Joselyn Chávez

Examples

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## 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
    )
}

regutools documentation built on May 2, 2020, 2:01 a.m.