background parameter in the peakAnnoEnrichment() function

[EraslanBas]

Hi,

In the peakAnnoEnrichment() function background parameter is defined as "A string that indicates whether to use a background set of matched peaks to compare against ("bgdPeaks") or all peaks ("all")." May I ask how these background set of matched peaks are computed? I get very different enrichment results when I change this parameter between "bgdPeaks" and "all".

Thanks in advance.

[rcorces]

background peaks are regions matched by GC content and accessibility

ArchR/R/MatrixDeviations.R

Lines 610 to 699 in f6c0388

	addBgdPeaks <- function(
	ArchRProj = NULL,
	nIterations = 50,
	w = 0.1,
	binSize = 50,
	seed = 1,
	method = "chromVAR",
	outFile = file.path(getOutputDirectory(ArchRProj), "Background-Peaks.rds"),
	force = FALSE
	){
	.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
	.validInput(input = nIterations, name = "nIterations", valid = c("integer"))
	.validInput(input = w, name = "w", valid = c("numeric"))
	.validInput(input = binSize, name = "binSize", valid = c("integer"))
	.validInput(input = seed, name = "seed", valid = c("integer"))
	.validInput(input = outFile, name = "outFile", valid = c("character"))
	.validInput(input = force, name = "force", valid = c("boolean"))
	if ("PeakMatrix" %ni% getAvailableMatrices(ArchRProj)) {
	.logMessage(paste0("PeakMatrix does not exist in the provided ArchRProject. Add a peak matrix using addPeakMatrix(). See available matrix names from getAvailableMatrices()!"), logFile = logFile)
	stop("PeakMatrix does not exist in the provided ArchRProject. Add a peak matrix using addPeakMatrix(). See available matrix names from getAvailableMatrices()!")
	}
	if(!is.null(metadata(getPeakSet(ArchRProj))$bgdPeaks) & !force){
	if(file.exists(metadata(getPeakSet(ArchRProj))$bgdPeaks)){
	stop("Background Peaks Already Exist! set force = TRUE to addBgdPeaks!")
	}else{
	if(force){
	message("Previous Background Peaks file does not exist! Identifying Background Peaks!")
	bgdPeaks <- .computeBgdPeaks(ArchRProj=ArchRProj, nIterations=nIterations, w=w, binSize=binSize, seed = seed, outFile = outFile, method = method)
	}else{
	stop("Previous Background Peaks file does not exist! set force = TRUE to addBgdPeaks!")
	}
	}
	}else{
	message("Identifying Background Peaks!")
	bgdPeaks <- .computeBgdPeaks(ArchRProj=ArchRProj, nIterations=nIterations, w=w, binSize=binSize, seed = seed, outFile = outFile, method = method)
	}
	if(length(getPeakSet(ArchRProj)) != nrow(bgdPeaks)){
	stop("Number of rows in Background Peaks does not match peakSet!")
	}
	metadata(ArchRProj@peakSet)$bgdPeaks <- outFile
	ArchRProj
	}
	#' Get Background Peaks from an ArchRProject
	#'
	#' This function will get/compute background peaks controlling for total accessibility and GC-content from an ArchRProject.
	#'
	#' @param ArchRProj An `ArchRProject` object.
	#' @param nIterations The number of background peaks to sample. See `chromVAR::getBackgroundPeaks()`.
	#' @param w The parameter controlling similarity measure of background peaks. See `chromVAR::getBackgroundPeaks()`.
	#' @param binSize The precision with which the similarity is computed. See `chromVAR::getBackgroundPeaks()`.
	#' @param 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.
	#' @param method A string indicating whether to use chromVAR or ArchR for background peak identification.
	#' @param force A boolean value indicating whether to force the file indicated by `outFile` to be overwritten if it already exists.
	#' @export
	getBgdPeaks <- function(
	ArchRProj = NULL,
	nIterations = 50,
	w = 0.1,
	binSize = 50,
	seed = 1,
	method = "chromVAR",
	force = FALSE
	){
	.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
	.validInput(input = nIterations, name = "nIterations", valid = c("integer"))
	.validInput(input = w, name = "w", valid = c("numeric"))
	.validInput(input = binSize, name = "binSize", valid = c("integer"))
	.validInput(input = seed, name = "seed", valid = c("integer"))