getChromLoc,FootprintFinder-method {trena} | R Documentation

## 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")

[Package trena version 1.12.1 Index]