getFootprintsInRegion: Get Footprints in a Region

getFootprintsInRegion,FootprintFinder-methodR 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 )

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.