filterOpenSea: Filter to open sea CpG loci

In JordanVeldboom/compartmap: A/B compartment inference from ATAC-seq and methylation array data

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)

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.