getChromLoc: Get Chromosome Location

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

Get Chromosome Location

Description

Using the gtf table in the genome database contained in a FootprintFinder object, get the locations of chromosomes with the specified gene name, biological unit type, and molecule type

Usage

## S4 method for signature 'FootprintFinder'
getChromLoc(obj, name, biotype = "protein_coding", moleculetype = "gene")

Arguments

obj	An object of class FootprintFinder
name	A gene name or ID
biotype	A type of biological unit (default="protein_coding")
moleculetype	A type of molecule (default="gene")

Value

A dataframe containing the results of a database query pertaining to the specified name, biotype, and molecule type. This dataframe contains the following columns: gene_id, gene_name, chr, start, endpos, strand

See Also

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

chrom.locs <- getChromLoc(fp, name = "MEF2C")

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