getRegulatoryChromosomalRegions,Trena-method {trena} | R Documentation

## Get the regulatory chromosomal regions for a Trena object

### Description

Get the regulatory chromosomal regions for a Trena object

### Usage

    ## S4 method for signature 'Trena'
    getRegulatoryChromosomalRegions(obj, chromosome,
      chromStart, chromEnd, regulatoryRegionSources, targetGene, targetGeneTSS,
      combine = FALSE)

### Arguments

`obj` | An object of class Trena
`chromosome` | A choromosome of interest
`chromStart` | The beginning of the desired region
`chromEnd` | The end of the desired region
`regulatoryRegionSources` | A vector containing the names of sources for chromosome information. These can be addresses of footprint databases or the names of DHS databases
`targetGene` | A target gene of interest
`targetGeneTSS` | An integer giving the location of the target gene's transcription start site
`combine` | A logical indicating whether or not to combine the output into one data frame (default = FALSE)

### Value

A list of regulatory regions for the supplied target gene. If `combine` is set to `TRUE`, the list is converted into a data frame.

### Examples

    # Get regulatory regions for MEF2C from a footprint database
    database.filename <- system.file(package="trena", "extdata", "mef2c.neigborhood.hg38.footprints.db")
    database.uri <- sprintf("sqlite://%s", database.filename)
    sources <- c(database.uri)

    trena <- Trena("hg38")
    chromosome <- "chr5"
    mef2c.tss <- 88904257
    loc.start <- mef2c.tss - 1000
    loc.end   <- mef2c.tss + 1000

    regions <- getRegulatoryChromosomalRegions(trena, chromosome, mef2c.tss-1000, mef2c.tss+1000,
    sources, "MEF2C", mef2c.tss)

    # Get regulatory regions for AQP4 from a Human DHS source
    trena <- Trena("hg38")
    aqp4.tss <- 26865884
    chromosome <- "chr18"
    sources <- c("encodeHumanDHS")

    regions <- getRegulatoryChromosomalRegions(trena, chromosome, aqp4.tss-1, aqp4.tss+3, sources, "AQP4", aqp4.tss)

[Package trena version 1.6.1 Index]