getRegulatoryChromosomalRegions: Get the regulatory chromosomal regions for a Trena object

In PriceLab/trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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)

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.