get_binding_sites {regutools} | R Documentation |
Retrieve the binding sites and genome location for a given transcription factor.
get_binding_sites(regulondb, transcription_factor, output_format = "GRanges")
regulondb |
A |
transcription_factor |
name of the transcription factor. |
output_format |
The output object. Can be either a |
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")