getPromoterRegionsAllGenes: Get Promoter Regions for All Genes

In PriceLab/trena-until-01mar2018: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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

## 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

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)

PriceLab/trena-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.