getPromoterRegionsAllGenes: Get Promoter Regions for All Genes

Description Usage Arguments Value See Also Examples

Description

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.

Usage

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## S4 method for signature '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, mapMotifsToTFsMergeIntoTable,FootprintFinder-method

Examples

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db.address <- system.file(package="TReNA", "extdata")
genome.db.uri <- paste("sqlite:/",db.address,"genome.sub.db", sep = "/")
project.db.uri <- paste("sqlite:/",db.address,"project.sub.db", sep = "/")
fp <- FootprintFinder(genome.db.uri, project.db.uri)

footprints <- getPromoterRegionsAllGenes(fp)

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.