Filter to open sea CpG loci

This function accepts a GRanges input of CpG islands that can be derived from UCSC table browser and rtracklayer::import(yourbed.bed)

Usage

filterOpenSea(obj, genome = c("hg19", "hg38", "mm10", "mm9"), other = NULL)

getOpenSeas(gr)

Arguments

obj

Input SummarizedExperiment or GRanges object

genome

Which genome to filter

other

GRanges of open sea regions (TODO)

gr

Input GRanges of CpG islands

Value

Filtered to open sea CpG loci

GRanges object that can be used with filterOpenSea()

Examples

if (requireNamespace("minfi", quietly = TRUE)) {
  data("array_data_chr14", package = "compartmap")
  opensea <- filterOpenSea(array.data.chr14, genome = "hg19")
}
#> Filtering to open sea CpG loci...

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