getGenePromoterRegion,FootprintFinder-method {trena} | R Documentation

## Get Gene Promoter Region

### Description

Using the `getChromLoc` function in conjunction with the gtf table inside the genome database specified by the FootprintFinder object, get the chromosome, starting location, and ending location for gene promoter region.

### Usage

    ## S4 method for signature 'FootprintFinder'
    getGenePromoterRegion(
      obj,
      gene,
      size.upstream = 1000,
      size.downstream = 0,
      biotype = "protein_coding",
      moleculetype = "gene"
    )

### Arguments

`obj` | An object of class FootprintFinder
`gene` | A gene name of ID
`size.upstream` | An integer denoting the distance upstream of the target gene to look for footprints (default = 1000)
`size.downstream` | An integer denoting the distance downstream of the target gene to look for footprints (default = 0)
`biotype` | A type of biological unit (default="protein_coding")
`moleculetype` | A type of molecule (default="gene")

### Value

A list containing 3 elements: 1) chr : The name of the chromosome containing the promoter region for the specified gene 2) start : The starting location of the promoter region for the specified gene 3) end : The ending location of the promoter region for the specified gene

### See Also

Other FootprintFinder methods: `FootprintFinder-class`, `closeDatabaseConnections,FootprintFinder-method`, `getChromLoc,FootprintFinder-method`, `getFootprintsForGene,FootprintFinder-method`, `getFootprintsInRegion,FootprintFinder-method`, `getGtfGeneBioTypes,FootprintFinder-method`, `getGtfMoleculeTypes,FootprintFinder-method`, `getPromoterRegionsAllGenes,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)

    prom.region <- getGenePromoterRegion(fp, gene = "MEF2C")

[Package trena version 1.16.0 Index]