getFootprintsInRegion: Get Footprints in a Region

Description Usage Arguments Value See Also Examples

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

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## 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

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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-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.