getATACABsignal {compartmap} | R Documentation

## Estimate A/B compartments from ATAC-seq 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")

[Package compartmap version 1.6.0 Index]