getGtfGeneBioTypes: Get the List of Biotypes

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

Get the List of Biotypes

Description

Using the gtf table in the genome database contained in a FootprintFinder object, get the list of different types of biological units (biotypes) contained in the table.

Usage

## S4 method for signature 'FootprintFinder'
getGtfGeneBioTypes(obj)

Arguments

obj	An object of class FootprintFinder

Value

A sorted list of the types of biological units contained in the gtf table of the genome database.

See Also

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

biotypes <- getGtfGeneBioTypes(fp)

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