getRegulatoryRegions: Get a table of regulatory regions for a Human DHS filter

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

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)

PriceLab/TReNA documentation built on March 21, 2023, 1:57 p.m.