FootprintFinder-class {trena} | R Documentation

## Class FootprintFinder

### Description

The FootprintFinder class is designed to query 2 supplied footprint databases (a genome database and a project database) for supplied genes or regions. Within the TReNA package, the FootprintFinder class is mainly used by the FootprintFilter class, but the FootprintFinder class offers more flexibility in constructing queries.

### Usage

    FootprintFinder(genome.database.uri, project.database.uri, quiet = TRUE)

### Arguments

`genome.database.uri` | The address of a genome database for use in filtering. This database must contain the tables "gtf" and "motifsgenes" at a minimum. The URI format is as follows: "dbtype://host/database" (e.g. "postgres://localhost/genomedb")
`project.database.uri` | The address of a project database for use in filtering. This database must contain the tables "regions" and "hits" at a minimum. The URI format is as follows: "dbtype://host/database" (e.g. "postgres://localhost/projectdb")
`quiet` | A logical denoting whether or not the FootprintFinder object should print output

### Value

An object of the FootprintFinder class

### Slots

`genome.db`

  The address of a genome database for use in filtering

`project.db`

  The address of a project database for use in filtering

`quiet`

  A logical argument denoting whether the FootprintFinder object should behave quietly

### See Also

`FootprintFilter`

Other FootprintFinder methods: `closeDatabaseConnections,FootprintFinder-method`, `getChromLoc,FootprintFinder-method`, `getFootprintsForGene,FootprintFinder-method`, `getFootprintsInRegion,FootprintFinder-method`, `getGenePromoterRegion,FootprintFinder-method`, `getGtfGeneBioTypes,FootprintFinder-method`, `getGtfMoleculeTypes,FootprintFinder-method`, `getPromoterRegionsAllGenes,FootprintFinder-method`

[Package trena version 1.16.0 Index]