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

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

Get Encode regulatory tables using a human DHS filter

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

## 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)
   getEncodeRegulatoryTableNames(hd.filter)
   
## End(Not run)

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