FootprintFilter-class {trena} | R Documentation

## Create a FootprintFilter object

### Description

A FootprintFilter object allows for filtering based on gene footprinting databases. Using its associated `getCandidates` method and URIs for both a genome database and project database, a FootprintFilter object can be used to filter a list of possible transcription factors to those that match footprint motifs for a supplied target gene.

### Usage

    FootprintFilter(genomeDB, footprintDB, regions = data.frame(),
      quiet = TRUE)

### Arguments

`genomeDB` | A connection to a database that contains genome information
`footprintDB` | A connection to a database that contains footprint information
`regions` | A data frame that specifies the regions of interest (default = data.frame())
`quiet` | A logical denoting whether or not the filter should print output

### Value

An object of the FootprintFilter class

### See Also

`getCandidates-FootprintFilter`

Other Filtering Objects: `VarianceFilter-class`

### Examples

    ## Not run:
       load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
       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 = "/")
       target.gene <- "MEF2C"
       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)

    ## End(Not run)

[Package trena version 1.6.1 Index]