getFootprintsInRegion: Get Footprints in a Region

In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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 )

trena documentation built on Nov. 15, 2020, 2:07 a.m.