Get Promoter Regions for All Genes

Using the gtf table inside the genome database specified by the FootprintFinder object, return the promoter regions for every protein-coding gene in the database.

# S4 method for FootprintFinder
getPromoterRegionsAllGenes(
  obj,
  size.upstream = 10000,
  size.downstream = 10000,
  use_gene_ids = TRUE
)

Arguments

obj	An object of class FootprintFinder
size.upstream	An integer denoting the distance upstream of each gene's transcription start site to include in the promoter region (default = 1000)
size.downstream	An integer denoting the distance downstream of each gene's transcription start site to include in the promoter region (default = 1000)
use_gene_ids	A binary indicating whether to return gene IDs or gene names (default = T)

Value

A GRanges object containing the promoter regions for all genes

See also

Other FootprintFinder methods: FootprintFinder-class, closeDatabaseConnections,FootprintFinder-method, getChromLoc,FootprintFinder-method, getFootprintsForGene,FootprintFinder-method, getFootprintsInRegion,FootprintFinder-method, getGenePromoterRegion,FootprintFinder-method, getGtfGeneBioTypes,FootprintFinder-method, getGtfMoleculeTypes,FootprintFinder-method

Examples

db.address <- system.file(package="trena", "extdata")
genome.db.uri <- paste("sqlite:/",db.address,"mef2c.neighborhood.hg38.gtfAnnotation.db", sep = "/")
project.db.uri <- paste("sqlite:/",db.address,"mef2c.neigborhood.hg38.footprints.db", sep = "/")
fp <- FootprintFinder(genome.db.uri, project.db.uri)

footprints <- getPromoterRegionsAllGenes(fp)