Whether the "arrow" files storage the result of ArchR projecet after perfoming filterDoublets function or not？

[Jane8166]

Hello everybody,

I filtered the cells with lower TSS and nFrags , and computed the Doublets score , and storaged the results as "project1";then I filtered the Doublets and saved the result as "project2".The cell number of project2 is lower the project1. But when I use the Arrowfiles from "project2" to create the new ArchR project "project3", the cell number of project3 is equal to the cell number of project1, what happened?

Thanks for your reply.

[rcorces]

If you look at the code for filterDoublets(), this works at the level of the ArchRProject and does not touch the Arrow files themselves.

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
	}

[Jane8166]

Thank you very much, I used the arrow of "project1" and refiltered the doublets, and this question has been resolved.