Get Footprints for Gene

Using the getGenePromoterRegion and getFootprintsInRegion functions in conjunction with the gtf table inside the genome database specified by the FootprintFinder object, retrieve a dataframe containing the footprints for a specified gene

# S4 method for FootprintFinder
getFootprintsForGene(
  obj,
  gene,
  size.upstream = 1000,
  size.downstream = 0,
  biotype = "protein_coding",
  moleculetype = "gene"
)

Arguments

obj	An object of class FootprintFinder
gene	A gene name of ID
size.upstream	An integer denoting the distance upstream of the target gene to look for footprints (default = 1000)
size.downstream	An integer denoting the distance downstream of the target gene to look for footprints (default = 0)
biotype	A type of biological unit (default="protein_coding")
moleculetype	A type of molecule (default="gene")

Value

A dataframe containing all footprints for the specified gene and accompanying parameters

See also

Other FootprintFinder methods: FootprintFinder-class, closeDatabaseConnections,FootprintFinder-method, getChromLoc,FootprintFinder-method, getFootprintsInRegion,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 <- getFootprintsForGene(fp, gene = "MEF2C")