filterOpenSea: Filter to open sea CpG loci

View source: R/utils.R

filterOpenSeaR Documentation

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

gr

Input GRanges of CpG islands

Value

Filtered to open sea CpG loci

GRanges object that can be used with filterOpenSea()

Examples

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 Oct. 18, 2023, 11:11 a.m.