get_dna_objects: Retrieve genomic elements from regulonDB

In regutools: regutools: an R package for data extraction from RegulonDB

Description

Retrieve genomic elements from regulonDB

Usage

get_dna_objects(
  regulondb,
  genome = "eschColi_K12",
  grange = GRanges("chr", IRanges(1, 5000)),
  elements = "gene"
)

Arguments

regulondb	A regulondb() object.
genome	A valid UCSC genome name.
grange	A GenomicRanges::GRanges-class() object indicating position left and right.
elements	A character vector specifying which annotation elements to plot. It can be any from: "-10 promoter box", "-35 promoter box", "gene", "promoter", "Regulatory Interaction", "sRNA interaction", or "terminator".

Value

GenomicRanges::GRanges-class() object with the elements found.

Author(s)

Joselyn Chavez

Examples

## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) {
      regulondb_conn <- connect_database()
  }

## Build the regulondb object
e_coli_regulondb <-
    regulondb(
        database_conn = regulondb_conn,
        organism = "chr",
        database_version = "1",
        genome_version = "1"
    )

## Get all genes from E. coli
get_dna_objects(e_coli_regulondb)

## Get genes providing Genomic Ranges
grange <- GenomicRanges::GRanges(
    "chr",
    IRanges::IRanges(5000, 10000)
)
get_dna_objects(e_coli_regulondb, grange)

## Get aditional elements within genomic positions
get_dna_objects(e_coli_regulondb,
    grange,
    elements = c("gene", "promoter")
)

regutools documentation built on Dec. 20, 2020, 2 a.m.