getRegulatoryChromosomalRegions,Trena-method | R Documentation |
Get the regulatory chromosomal regions for a Trena object
## S4 method for signature 'Trena' getRegulatoryChromosomalRegions( obj, chromosome, chromStart, chromEnd, regulatoryRegionSources, targetGene, targetGeneTSS, combine = FALSE )
obj |
An object of class Trena |
chromosome |
A choromosome of interest |
chromStart |
The beginning of the desired region |
chromEnd |
The end of the desired region |
regulatoryRegionSources |
A vector containing the names of sources for chromosome information. These can be addresses of footprint databases or the names of DHS databases |
targetGene |
A target gene of interest |
targetGeneTSS |
An integer giving the location of the target gene's transcription start site |
combine |
A logical indicating whether or not to combine the output into one data frame (default = FALSE) |
A list of regulatory regions for the supplied target gene. If combine
is set to TRUE
,
the list is converted into a data frame.
# Get regulatory regions for MEF2C from a footprint database database.filename <- system.file(package="trena", "extdata", "mef2c.neigborhood.hg38.footprints.db") database.uri <- sprintf("sqlite://%s", database.filename) sources <- c(database.uri) trena <- Trena("hg38") chromosome <- "chr5" mef2c.tss <- 88904257 loc.start <- mef2c.tss - 1000 loc.end <- mef2c.tss + 1000 #regions <- getRegulatoryChromosomalRegions(trena, chromosome, mef2c.tss-1000, mef2c.tss+1000, # sources, "MEF2C", mef2c.tss) # Get regulatory regions for AQP4 from a Human DHS source trena <- Trena("hg38") aqp4.tss <- 26865884 chromosome <- "chr18" sources <- c("encodeHumanDHS") #regions <- getRegulatoryChromosomalRegions(trena, chromosome, aqp4.tss-1, aqp4.tss+3, sources, "AQP4", aqp4.tss)
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