what is the standard about how ArchR automatically annotated peaks

[l-magnificence]

Who know how ArchR defined peaks as promoters and distal type? Thank you!

[rcorces]

That code is in .fastAnnoPeaks(). It is based on overlap with annotations present in your geneAnnotation

ArchR/R/ReproduciblePeakSet.R

Lines 604 to 653 in 381842c

	.fastAnnoPeaks <- function(
	peaks = NULL,
	BSgenome = NULL,
	geneAnnotation = NULL,
	promoterRegion = c(2000, 100),
	logFile = NULL
	){
	#Validate
	peaks <- .validGRanges(peaks)
	peakSummits <- GenomicRanges::resize(peaks,1,"center")
	geneAnnotation$genes <- .validGRanges(geneAnnotation$genes)
	geneAnnotation$exons <- .validGRanges(geneAnnotation$exons)
	geneAnnotation$TSS <- .validGRanges(geneAnnotation$TSS)
	BSgenome <- validBSgenome(BSgenome)
	#First Lets Get Distance to Nearest Gene Start
	.logMessage("Annotating Peaks : Nearest Gene", logFile = logFile)
	distPeaks <- distanceToNearest(peakSummits, GenomicRanges::resize(geneAnnotation$genes, 1, "start"), ignore.strand = TRUE)
	mcols(peaks)$distToGeneStart <- mcols(distPeaks)$distance
	mcols(peaks)$nearestGene <- mcols(geneAnnotation$genes)$symbol[subjectHits(distPeaks)]
	.logMessage("Annotating Peaks : Gene", logFile = logFile)
	promoters <- extendGR(GenomicRanges::resize(geneAnnotation$genes, 1, "start"), upstream = promoterRegion[1], downstream = promoterRegion[2])
	op <- overlapsAny(peakSummits, promoters, ignore.strand = TRUE)
	og <- overlapsAny(peakSummits, geneAnnotation$genes, ignore.strand = TRUE)
	oe <- overlapsAny(peakSummits, geneAnnotation$exons, ignore.strand = TRUE)
	type <- rep("Distal", length(peaks))
	type[which(og & oe)] <- "Exonic"
	type[which(og & !oe)] <- "Intronic"
	type[which(op)] <- "Promoter"
	mcols(peaks)$peakType <- type
	#First Lets Get Distance to Nearest TSS's
	.logMessage("Annotating Peaks : TSS", logFile = logFile)
	distTSS <- distanceToNearest(peakSummits, GenomicRanges::resize(geneAnnotation$TSS, 1, "start"), ignore.strand = TRUE)
	mcols(peaks)$distToTSS <- mcols(distTSS)$distance
	if("symbol" %in% colnames(mcols(geneAnnotation$TSS))){
	mcols(peaks)$nearestTSS <- mcols(geneAnnotation$TSS)$symbol[subjectHits(distTSS)]
	}else if("tx_name" %in% colnames(mcols(geneAnnotation$TSS))){
	mcols(peaks)$nearestTSS <- mcols(geneAnnotation$TSS)$tx_name[subjectHits(distTSS)]
	}
	#Get NucleoTide Content
	.logMessage("Annotating Peaks : GC", logFile = logFile)
	nucFreq <- BSgenome::alphabetFrequency(getSeq(BSgenome, peaks))
	mcols(peaks)$GC <- round(rowSums(nucFreq[,c("G","C")]) / rowSums(nucFreq),4)
	mcols(peaks)$N <- round(nucFreq[,c("N")] / rowSums(nucFreq),4)
	peaks
	}