get_binding_sites: Get the binding sites for a Transcription Factor (TF)
In regutools: regutools: an R package for data extraction from RegulonDB

Description Usage Arguments Value Author(s) Examples

Retrieve the binding sites and genome location for a given transcription factor.

1	get_binding_sites(regulondb, transcription_factor, output_format = "GRanges")

`regulondb`	A `regulondb()` object.
`transcription_factor`	name of the transcription factor.
`output_format`	The output object. Can be either a `GRanges` (default) or `Biostrings`.

Either a GRanges object or a Biostrings object summarizing information about the binding sites of the transcription factors.

José Alquicira Hernández, Jacques van Helden, 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"
    )

## Get the binding sites for AraC
get_binding_sites(e_coli_regulondb, transcription_factor = "AraC")