Get Background Peaks from an ArchRProject

This function will get/compute background peaks controlling for total accessibility and GC-content from an ArchRProject.

getBgdPeaks(
  ArchRProj = NULL,
  nIterations = 50,
  w = 0.1,
  binSize = 50,
  seed = 1,
  method = "chromVAR",
  force = FALSE
)

Arguments

ArchRProj

An ArchRProject object.

nIterations

The number of background peaks to sample. See chromVAR::getBackgroundPeaks().

w

The parameter controlling similarity measure of background peaks. See chromVAR::getBackgroundPeaks().

binSize

The precision with which the similarity is computed. See chromVAR::getBackgroundPeaks().

seed

A number to be used as the seed for random number generation. It is recommended to keep track of the seed used so that you can reproduce results downstream.

method

A string indicating whether to use chromVAR or ArchR for background peak identification.

force

A boolean value indicating whether to force the file indicated by outFile to be overwritten if it already exists.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Get Background Peaks
bgdPeaks <- getBgdPeaks(proj, force = TRUE)