HumanDHSFilter-class {trena} | R Documentation

## Create a HumanDHSFilter object

### Description

A HumanDHSFilter object allows for filtering based on DNAse hypersensitivity (DHS) data. Its associated `getCandidates` method uses a genome from a BSgenome database (either hg19 or hg38), DNA region specifications, and (variants/pfms,encodetablename, match to filter a list of possible regulators factors to those that match the supplied criteria.

### Usage

    HumanDHSFilter(
      genomeName,
      encodeTableName = "wgEncodeRegDnaseClustered",
      pwmMatchPercentageThreshold,
      geneInfoDatabase.uri,
      regions,
      variants = NA_character_,
      pfms,
      quiet = TRUE
    )

### Arguments

`genomeName` | A character string indicating the reference genome; currently, the only accepted strings are "hg38" and "hg19", both of which are human genomes.
`encodeTableName` | (default = "wgEncodeRegDnaseClustered")
`pwmMatchPercentageThreshold` | A numeric from 0-100 to serve as a threshold for a match
`geneInfoDatabase.uri` | An address for a gene database
`regions` | A data frame containing the regions of interest
`variants` | A character vector containing a list of variants
`pfms` | A list of position frequency matrices, often converted from a MotifList object created by a MotifDb query
`quiet` | A logical denoting whether or not the solver should print output

### Value

A CandidateFilter class object that filters using Human DHS data

### See Also

`getCandidates-HumanDHSFilter`,

Other Solver class objects: `BayesSpikeSolver`, `EnsembleSolver`, `LassoPVSolver`, `LassoSolver`, `PearsonSolver`, `RandomForestSolver`, `RidgeSolver`, `Solver-class`, `SpearmanSolver`, `XGBoostSolver`

### Examples

    if(interactive()) { # takes too long in the bioc windows build
      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 = "/")

        # 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 = as.list(query(query(MotifDb, "sapiens"),"jaspar2016")))
       } # if interactive

[Package trena version 1.10.2 Index]