Gather open sea CpG from a GRanges of CpG islands

This function accepts a GRanges input of CpG islands that can be derived from UCSC table browser and rtracklayer::import(yourbed.bed). It resizes the inteval to create 4kb flanking open sea regions around the CpG islands as defined by Fortin and Hansen (Genome Biology, 2015).

Usage

getOpenSeas(gr)

Arguments

gr

Input GRanges of CpG islands

Value

GRanges object that can be used with filterOpenSea()

Examples

#cpgi <- rtracklayer::import(system.file("inst/extdata/mm10_cpgi.bed", package = "compartmap"))
#opensea_cpg <- getOpenSeas(cpgi)