getATACABsignal {compartmap} | R Documentation

## Estimate A/B compartments from ATAC-seq data

### Description

`getATACABsignal` returns estimated A/B compartments from ATAC-seq data.

### Usage

    getATACABsignal(
      obj,
      res = 1e+06,
      parallel = FALSE,
      chr = NULL,
      targets = NULL,
      cores = 2,
      bootstrap = TRUE,
      num.bootstraps = 100,
      genome = c("hg19", "hg38", "mm9", "mm10"),
      other = NULL,
      group = FALSE,
      boot.parallel = FALSE,
      boot.cores = 2
    )

    getRNAABsignal(
      obj,
      res = 1e+06,
      parallel = FALSE,
      chr = NULL,
      targets = NULL,
      cores = 2,
      bootstrap = TRUE,
      num.bootstraps = 100,
      genome = c("hg19", "hg38", "mm9", "mm10"),
      other = NULL,
      group = FALSE,
      boot.parallel = FALSE,
      boot.cores = 2
    )

### Arguments

`obj` | Input SummarizedExperiment object
`res` | Compartment resolution in bp
`parallel` | Whether to run samples in parallel
`chr` | What chromosome to work on (leave as NULL to run on all chromosomes)
`targets` | Samples/cells to shrink towards
`cores` | How many cores to use when running samples in parallel
`bootstrap` | Whether we should perform bootstrapping of inferred compartments
`num.bootstraps` | How many bootstraps to run
`genome` | What genome to work on ("hg19", "hg38", "mm9", "mm10")
`other` | Another arbitrary genome to compute compartments on
`group` | Whether to treat this as a group set of samples
`boot.parallel` | Whether to run the bootstrapping in parallel
`boot.cores` | How many cores to use for the bootstrapping

### Value

A RaggedExperiment of inferred compartments

### Functions

- `getRNAABsignal`: Alias for getATACABsignal

### Examples

    data("k562_scatac_chr14", package = "compartmap")
    atac_compartments <- getATACABsignal(k562_scatac_chr14, parallel=FALSE, chr="chr14", bootstrap=FALSE, genome="hg19", group = TRUE)

[Package compartmap version 1.10.0 Index]