getArrayABsignal: Estimate A/B compartments from methylation array data

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

Description

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

Usage

getArrayABsignal(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	Specific chromosomes to analyze
targets	Specify samples to use as shrinkage targets
...	Additional arguments

Details

This function is modified from the minfi::compartments to infer A/B compartments from array data

Value

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

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