increased the limit (9247d975) · Commits · github_fork / ZUMIs

zUMIs-dge.R

+5 −5

Original line number	Diff line number	Diff line
		@@ -195,9 +195,9 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		reads <- tibble(XC=substring(reads$V1, bcstart, bcend),XM=substring(reads$V1, umistart, umiend),GE=fctsfile$V1)
		}
		if(is.numeric(bcfile)){
		if(bcfile>10000){
		print("Attention! I limited your cell barcodes to 10000!")
		bcfile <- 10000
		if(bcfile>25000){
		print("Attention! I limited your cell barcodes to 25000!")
		bcfile <- 25000
		}
		bc <- reads %>% group_by(XC) %>% dplyr::summarise(n=length(XM)) %>% top_n(bcfile) %>% dplyr::select(V1=XC)
		}else if(is.na(bcfile)){
		@@ -211,9 +211,9 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		fullstats_detected<- fullstats[which(fullstats$deltarel>0.001),]
		}

		if(nrow(fullstats_detected)>10000){
		if(nrow(fullstats_detected)>25000){
		print("Attention! I could not adaptively determine the real cell barcodes!")
		bc <- reads %>% group_by(XC) %>% top_n(10000) %>% dplyr::select(V1=XC)
		bc <- reads %>% group_by(XC) %>% top_n(25000) %>% dplyr::select(V1=XC)
		fullstats_detected<- fullstats[which(fullstats$XC %in% bc$V1),]
		}else if(nrow(fullstats_detected)<10){
		print("Attention! I could not adaptively determine the real cell barcodes!")