getChromLoc: Get Chromosome Location

Description Usage Arguments Value See Also Examples

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

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## 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

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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-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.