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

In PriceLab/trena-until-01mar2018: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

Get a tabel 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-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.