getCandidates,FootprintFilter-method {trena} | R Documentation

## Get candidate genes using the footprint filter

### Description

Get candidate genes using the footprint filter

### Usage

    ## S4 method for signature 'FootprintFilter'
    getCandidates(obj)

### Arguments

`obj` | An object of class FootprintFilter

### Value

A list, where one element is the transcription factors found in the footprints and the other is a data frame containing all the meta data for the footprints

### See Also

`FootprintFilter`

Other getCandidate Methods: `getCandidates,GeneOntologyFilter-method`, `getCandidates,HumanDHSFilter-method`, `getCandidates,VarianceFilter-method`, `getCandidates()`

### Examples

    # Use footprint filter with the included SQLite database for MEF2C to filter candidates
    # in the included Alzheimer's dataset, using the Trena object to get regions
    ## Not run:
       target.gene <- "MEF2C"
       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 = "/")
       size.upstream <- 1000
       size.downstream <- 1000
          # Construct a Trena object and use it to retrive the regions
       trena <- Trena("hg38")
       regions <- getProximalPromoter(trena,target.gene, size.upstream, size.downstream)
       footprint.filter <- FootprintFilter(genomeDB = genome.db.uri, footprintDB = project.db.uri,
                                           regions = regions)
       footprints <- getCandidates(footprint.filter)

    ## End(Not run)

[Package trena version 1.12.1 Index]