get_binding_sites: Get the binding sites for a Transcription Factor (TF)

Description Usage Arguments Value Author(s) Examples

View source: R/get_binding_sites.R

Description

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

Usage

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

Arguments

regulondb

A regulondb() object.

transcription_factor

name of the transcription factor.

output_format

The output object. Can be either a GRanges (default) or Biostrings.

Value

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

Author(s)

José Alquicira Hernández, Jacques van Helden, 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"
    )

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

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