filterOpenSea: Filter to open sea CpG loci

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Filter to open sea CpG loci

Description

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 (require(minfi)) {
  data("meth_array_450k_chr14", package = "compartmap")
  opensea <- filterOpenSea(array.data.chr14, genome = "hg19")
}
#cpgi <- rtracklayer::import(system.file("inst/extdata/mm10_cpgi.bed", package = "compartmap"))
#opensea_cpg <- getOpenSeas(cpgi)

biobenkj/compartmap documentation built on Feb. 21, 2025, 9:14 p.m.