getATACABsignal: Estimate A/B compartments from ATAC-seq data

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

Description

getATACABsignal returns estimated A/B compartments from methylation array data.

Usage

getATACABsignal(obj, res = 1e+06, parallel = FALSE, allchrs = FALSE,
  chr = NULL, targets = NULL, ...)

Arguments

obj	Input GenomicRatioSet object
res	Compartment resolution (in bp)
parallel	Should the inference be done in parallel?
allchrs	Whether all autosomes should be used for A/B inference
chr	Specify a chromosome to analyze
targets	Specify samples as shrinkage targets
...	Additional arguments

Details

This function estimates A/B compartments shrinking towards a global mean of targets or across samples

Value

A p x n matrix (samples as columns and compartments as rows) of compartments

Examples

library(GenomicRanges)
library(SummarizedExperiment)
library(Homo.sapiens)

data(bulkATAC_raw_filtered_chr14, package = "compartmap")
atac_compartments <- getATACABsignal(filtered.data.chr14, chr = "chr14", genome = "hg19")

compartmap documentation built on Nov. 8, 2020, 5:34 p.m.