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

View source: R/getATACABsignal.R

getATACABsignalR 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)

biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.