predictionCutoff parameter in addPeak2GeneLinks

[RegnerM2015]

Hi @rcorces and @jeffmgranja ,

I was looking at the source code for addPeak2GeneLinks and the use of predictionCutoff:

ArchR/R/IntegrativeAnalysis.R

Lines 1035 to 1057 in f6c0388

	dfAll <- .safelapply(seq_along(ArrowFiles), function(x){
	cNx <- paste0(names(ArrowFiles)[x], "#", h5read(ArrowFiles[x], paste0(useMatrix, "/Info/CellNames")))
	pSx <- tryCatch({
	h5read(ArrowFiles[x], paste0(useMatrix, "/Info/predictionScore"))
	}, error = function(e){
	if(getArchRVerbose()) message("No predictionScore found. Continuing without predictionScore!")
	rep(9999999, length(cNx))
	})
	DataFrame(
	cellNames = cNx,
	predictionScore = pSx
	)
	}, threads = threads) %>% Reduce("rbind", .)
	.logDiffTime(
	sprintf("Filtered Low Prediction Score Cells (%s of %s, %s)",
	sum(dfAll[,2] < predictionCutoff),
	nrow(dfAll),
	round(sum(dfAll[,2] < predictionCutoff) / nrow(dfAll), 3)
	), t1=tstart, verbose=verbose, logFile=logFile)
	keep <- sum(dfAll[,2] >= predictionCutoff) / nrow(dfAll)
	dfAll <- dfAll[which(dfAll[,2] > predictionCutoff),]

It appears that the predictionCutoff is used to subset dfAll but is not used later on when making metacells. The object dfAll is also not used later on. If I am misinterpreting, if you could point me in the direction of where predictionCutoff is used to subset out cells, that would be greatly appreciated! Thank you for your help.

[rcorces]

Thanks for posting this and sorry it has taken me a while to look into this. I see exactly what you see. I imagine this is a bug but will have to look into it more. I'm migrating this to an Issue for tracking purposes.

[RegnerM2015]

No worries! Thanks for checking into it.

It could be convenient to create the subset of cells meeting the predictionCutoff here (similar to cellsToUse):

ArchR/R/IntegrativeAnalysis.R

Lines 1070 to 1074 in f6c0388

	#Get Reduced Dims
	rD <- getReducedDims(ArchRProj, reducedDims = reducedDims, corCutOff = corCutOff, dimsToUse = dimsToUse)
	if(!is.null(cellsToUse)){
	rD <- rD[cellsToUse, ,drop=FALSE]
	}