getRegulatoryRegions,HumanDHSFilter-method {trena} | R Documentation

## Get a table of regulatory regions for a Human DHS filter

### Description

Get a table of regulatory regions for a Human DHS filter

### Usage

    ## S4 method for signature 'HumanDHSFilter'
    getRegulatoryRegions(
      obj,
      encode.table.name,
      chromosome,
      start,
      end,
      score.threshold = 0
    )

### Arguments

`obj` | An object of class HumanDHSFilter
`encode.table.name` | A vector of names for Encode tables
`chromosome` | The chromosome of interest
`start` | The starting position
`end` | The ending position
`score.threshold` | A threshold for the score (default = 200)

### Value

A data frame containing the regulatory regions for the filter, including the chromosome, start, and end positions, plus the count and score of each region.

### See Also

`HumanDHSFilter`

### Examples

    ## Not run:
    # Make a filter for "transcription, DNA-templated" and use it to filter candidates
    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)

    chrom <- "chr2"
    rs13384219.loc <- 57907323
    start <- rs13384219.loc - 10
    end <- rs13384219.loc + 10

    tableNames <- getEncodeRegulatoryTableNames(hd.filter)

    getRegulatoryRegions(hd.filter, tableNames[1], chrom, start, end)

    ## End(Not run)

[Package trena version 1.16.0 Index]