getCandidates-HumanDHSFilter-method: Get candidate genes using a human DHS filter

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

Get candidate genes using a human DHS filter

Description

Get candidate genes using a human DHS filter

Usage

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

Arguments

obj	An object of class FootprintFilter

Value

A list, where one element a character vector of transcription factors that match the GO term and the other is an empty data frame.

See Also

FootprintFilter

Other getCandidate Methods: getCandidates,FootprintFilter-method, getCandidates,GeneOntologyFilter-method, getCandidates,VarianceFilter-method, getCandidates()

Examples

# Make a filter for "transcription, DNA-templated" and use it to filter candidates
## Not run: 
#' 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)

getCandidates(hd.filter)

## End(Not run)

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