getEncodeRegulatoryTableNames,HumanDHSFilter-method {trena} | R Documentation

## Get Encode regulatory tables using a human DHS filter

### Description

Get Encode regulatory tables using a human DHS filter

### Usage

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

### Arguments

`obj` | An object of class HumanDHSFilter

### Value

A character vector containing the names of the Encode regulatory tables for the regions contained in the HumanDHSFilter object

### See Also

`HumanDHSFilter`

### Examples

    ## 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)
       getEncodeRegulatoryTableNames(hd.filter)

    ## End(Not run)

[Package trena version 1.6.1 Index]