modified dge downsampling (834cb99d) · Commits · github_fork / ZUMIs

zUMIs-dge.R

+2 −2

Original line number	Diff line number	Diff line
		@@ -249,7 +249,7 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		subsampling_min <- as.numeric(strsplit(subsampling_iter,"-")[[1]][1])
		subsampling_max <- as.numeric(strsplit(subsampling_iter,"-")[[1]][2])

		if(as.logical((reads %>% group_by(XC) %>% dplyr::summarise(n=length(XM)) %>% top_n(1))[,2] >= subsampling_min)==TRUE){
		if(as.logical((nrow(reads %>% group_by(XC) %>% dplyr::summarise(n=length(XM)) %>% filter(n>=subsampling_min))) >= 2)==TRUE){
		print(paste("I am subsampling to ",subsampling_iter,sep=""))
		tmp1 <- reads %>% dplyr::filter(XC %in% bc$V1) %>% group_by(XC) %>% filter(length(XC) > subsampling_max) %>% dplyr::sample_n(size = subsampling_max,replace=F)%>% dplyr::filter(GE!="*") %>% group_by(XC,GE) %>% summarise(umicount=length(unique(XM)),readcount=length(XM))
		tmp2 <- reads %>% dplyr::filter(XC %in% bc$V1) %>% group_by(XC) %>% filter((length(XC) < subsampling_max) & (length(XC) >= subsampling_min))%>% dplyr::filter(GE!="*") %>% group_by(XC,GE) %>% summarise(umicount=length(unique(XM)),readcount=length(XM))
		@@ -259,7 +259,7 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		}
		}else{
		subsampling_no <- as.numeric(subsampling_iter)
		if(as.logical((reads %>% group_by(XC) %>% dplyr::summarise(n=length(XM)) %>% top_n(1))[,2] >= subsampling_no)==TRUE){
		if(as.logical((nrow(reads %>% group_by(XC) %>% dplyr::summarise(n=length(XM)) %>% filter(n>=subsampling_no))) >= 2)==TRUE){
		print(paste("I am subsampling to ",subsampling_iter,sep=""))
		umicounts_sub <- reads %>% dplyr::filter(XC %in% bc$V1) %>% group_by(XC) %>% filter(length(XC) >= subsampling_no) %>% dplyr::sample_n(size = subsampling_no,replace=F)%>% dplyr::filter(GE!="*") %>% group_by(XC,GE) %>% summarise(umicount=length(unique(XM)),readcount=length(XM))

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