getGenePromoterRegion: Get Gene Promoter Region

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

Get Gene Promoter Region

Description

Using the getChromLoc function in conjunction with the gtf table inside the genome database specified by the FootprintFinder object, get the chromosome, starting location, and ending location for gene promoter region.

Usage

## S4 method for signature 'FootprintFinder'
getGenePromoterRegion(
  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 list containing 3 elements: 1) chr : The name of the chromosome containing the promoter region for the specified gene 2) start : The starting location of the promoter region for the specified gene 3) end : The ending location of the promoter region for the specified gene

See Also

Other FootprintFinder methods: FootprintFinder-class, closeDatabaseConnections,FootprintFinder-method, getChromLoc,FootprintFinder-method, getFootprintsForGene,FootprintFinder-method, getFootprintsInRegion,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)

prom.region <- getGenePromoterRegion(fp, gene = "MEF2C")

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