getPromoterRegionsAllGenes,FootprintFinder-method {trena} | R Documentation

## Get Promoter Regions for All Genes

### 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)

[Package trena version 1.12.1 Index]