getEncodeRegulatoryTableNames-HumanDHSFilter: Get Encode regulatory tables using a human DHS filter

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

Description

Get Encode regulatory tables using a human DHS filter

Usage

## S4 method for signature 'HumanDHSFilter'
getEncodeRegulatoryTableNames(obj)

Arguments

obj	An object of class HumanDHSFilter

Value

A character vector containing the names of the Encode regulatory tables for the regions contained in the HumanDHSFilter object

See Also

HumanDHSFilter

Examples

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)

getEncodeRegulatoryTableNames(hd.filter) 

PriceLab/trena-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.