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 1.4.0 Index]