getGtfGeneBioTypes,FootprintFinder-method {trena} | R Documentation

## Get the List of Biotypes

### Description

Using the gtf table in the genome database contained in a FootprintFinder object, get the list of different types of biological units (biotypes) contained in the table.

### Usage

    ## S4 method for signature 'FootprintFinder'
    getGtfGeneBioTypes(obj)

### Arguments

`obj` | An object of class FootprintFinder

### Value

A sorted list of the types of biological units contained in the gtf table of the genome database.

### See Also

Other FootprintFinder methods: `FootprintFinder-class`, `closeDatabaseConnections,FootprintFinder-method`, `getChromLoc,FootprintFinder-method`, `getFootprintsForGene,FootprintFinder-method`, `getFootprintsInRegion,FootprintFinder-method`, `getGenePromoterRegion,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)

    biotypes <- getGtfGeneBioTypes(fp)

[Package trena version 1.16.0 Index]