getFootprintsInRegion,FootprintFinder-method {trena} | R Documentation

## Get Footprints in a Region

### Description

Using the regions and hits tables inside the project database specified by the FootprintFinder object, return the location, chromosome, starting position, and ending positions of all footprints for the specified region.

### Usage

    ## S4 method for signature 'FootprintFinder'
    getFootprintsInRegion(obj, chromosome, start, end)

### Arguments

`obj` | An object of class FootprintFinder
`chromosome` | The name of the chromosome of interest
`start` | An integer denoting the start of the desired region
`end` | An integer denoting the end of the desired region

### Value

A dataframe containing all footprints for the specified region

### See Also

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

    footprints <- getFootprintsInRegion(fp, chromosome = "chr5",
    start = 88903305, end = 88903319 )

[Package trena version 1.12.1 Index]