Doublets

[Guliariel]

Hello,
I am looking to get the list of the excluded cells/barcodes after Doublets filtering.
Where can I get this information from?
Thank you!
ArchR is such a great tool :)

[rcorces]

if you have already run filterDoublets() then the cells that were found to be doublets will have been removed from cellColData so you cant see them any more.
Prior to running filterDoublets() you just need to check cellColData to see which cells dont meet the criteria (cutEnrich, cutScore, filterRatio) you will using during filterDoublets(). You can always read the code in filterDoublets to understand this better.

ArchR/R/FilterCells.R

Lines 45 to 106 in 968e442

	filterDoublets <- function(ArchRProj = NULL, cutEnrich = 1, cutScore = -Inf, filterRatio = 1){
	.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
	.validInput(input = cutEnrich, name = "cutEnrich", valid = c("numeric"))
	.validInput(input = cutScore, name = "cutScore", valid = c("numeric"))
	.validInput(input = filterRatio, name = "filterRatio", valid = c("numeric"))
	if(any(grepl("filterDoublets", names(ArchRProj@projectSummary)))){
	stop("Already ran filterDoublets on ArchRProject! Cannot be re-ran on an ArchRProject!")
	}
	df <- getCellColData(ArchRProj, c("Sample", "DoubletEnrichment", "DoubletScore"))
	splitDF <- split(seq_len(nrow(df)), as.character(df$Sample))
	cellsFilter <- lapply(splitDF, function(y){
	x <- df[y, ,drop = FALSE]
	n <- nrow(x)
	x <- x[order(x$DoubletEnrichment, decreasing = TRUE), ]
	if(!is.null(cutEnrich)){
	x <- x[which(x$DoubletEnrichment >= cutEnrich), ]
	}
	if(!is.null(cutScore)){
	x <- x[which(x$DoubletScore >= cutScore), ]
	}
	if(nrow(x) > 0){
	head(rownames(x), filterRatio * n * (n / 100000))
	}else{
	NULL
	}
	}) %>% unlist(use.names=FALSE)
	message("Filtering ", length(cellsFilter), " cells from ArchRProject!")
	tabRemove <- table(df[cellsFilter,]$Sample)
	tabAll <- table(df$Sample)
	samples <- unique(df$Sample)
	for(i in seq_along(samples)){
	if(!is.na(tabRemove[samples[i]])){
	message("\t", samples[i], " : ", tabRemove[samples[i]], " of ", tabAll[samples[i]], " (", round(100 * tabRemove[samples[i]] / tabAll[samples[i]], 1),"%)")
	}else{
	message("\t", samples[i], " : ", 0, " of ", tabAll[samples[i]], " (0%)")
	}
	}
	if(length(cellsFilter) > 0){
	ArchRProj@cellColData <- ArchRProj@cellColData[rownames(ArchRProj@cellColData) %ni% cellsFilter,,drop=FALSE]
	}
	ArchRProj <- addProjectSummary(ArchRProj = ArchRProj, name = "filterDoublets",
	summary = c(cutEnrich = cutEnrich, cutScore = cutScore, filterRatio = filterRatio))
	ArchRProj
	}