getFootprintsForGene: Get Footprints for Gene

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

Description

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

Usage

## S4 method for signature '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")

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