fixed automatic BC selection (baed3523) · Commits · github_fork / ZUMIs

zUMIs-dge.R

+11 −10

Original line number	Diff line number	Diff line
		@@ -204,9 +204,10 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		}

		BCselection <- function(fullstats){
		tmp<-mclust::Mclust(log10(fullstats$nreads))
		tmp<-mclust::Mclust(log10(fullstats$nreads), modelNames = c("E","V"))
		ss <- ifelse(tmp$modelName=="E",1,tmp$G)
		mm<-tmp$parameters$mean[tmp$G]
		va<-tmp$parameters$variance$sigmasq[tmp$G]
		va<-tmp$parameters$variance$sigmasq[ss]

		cut<-10^(qnorm(0.01, m=mm,sd=sqrt(va)))
		rcfilt <- fullstats[fullstats$nreads>=cut,]
		@@ -234,13 +235,8 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,
		reads <- tibble(XC=substring(reads$V1, bcstart, bcend),XM=substring(reads$V1, umistart, umiend),GE=fctsfile$V1)
		}

		if(is.na(bcfile) \|\| is.numeric(bcfile)){
		if(is.numeric(bcfile)){
		fullstats <- reads %>% group_by(XC) %>% dplyr::summarise(nreads=length(XM)) %>% top_n(bcfile)
		}else{
		if(is.na(bcfile)){
		fullstats <- reads %>% group_by(XC) %>% summarise(nreads=length(XM))
		}

		fullstats<-fullstats[fullstats$nreads>=nReadsBC,]
		fullstats <- fullstats[order(fullstats$nreads,decreasing = T),]
		fullstats$cs <- cumsum(fullstats$nreads)
		@@ -268,9 +264,14 @@ makeGEprofile <- function(abamfile,ubamfile,bcfile,safannot,ncores,stra,bcstart,

		ggsave(bcplot,filename=paste(out,"/zUMIs_output/stats/",sn,".detected_cells.pdf",sep=""),width = 10,height = 4)

		}else{
		if(is.numeric(bcfile)){
		fullstats_detected <- reads %>% group_by(XC) %>% dplyr::summarise(nreads=length(XM)) %>% top_n(bcfile)
		bc <- data.frame(V1=fullstats_detected$XC)
		}else{
		bc <- read.table(bcfile,header = F,stringsAsFactors = F)
		}
		}

		cluster <- create_cluster(ncores)
		set_default_cluster(cluster)

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