getCandidates,HumanDHSFilter-method {trena} | R Documentation

## Get candidate genes using a human DHS filter

### Description

Get candidate genes using a human DHS filter

### Usage

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

### Arguments

`obj` | An object of class FootprintFilter

### Value

A list, where one element a character vector of transcription factors that match the GO term and the other is an empty data frame.

### See Also

`FootprintFilter`

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

### Examples

    # Make a filter for "transcription, DNA-templated" and use it to filter candidates
    ## Not run:
    #' load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
    targetGene <- "VRK2"
    promoter.length <- 1000
    genomeName <- "hg38"
    db.address <- system.file(package="trena", "extdata")
    genome.db.uri    <- paste("sqlite:/", db.address, "vrk2.neighborhood.hg38.gtfAnnotation.db",  sep = "/")
    jaspar.human <- as.list(query(query(MotifDb, "sapiens"),"jaspar2016"))

    # Grab regions for VRK2 using shoulder size of 1000
    trena <- Trena(genomeName)
    tbl.regions <- getProximalPromoter(trena, "VRK2", 1000, 1000)

    hd.filter <- HumanDHSFilter(genomeName, pwmMatchPercentageThreshold = 85,
    geneInfoDatabase.uri = genome.db.uri, regions = tbl.regions, pfms = jaspar.human)

    getCandidates(hd.filter)

    ## End(Not run)

[Package trena version 1.12.1 Index]