modified dturtle.R in R (e75cb3e2) · Commits · Chaos / chaos.tools

R/dturtle.R

+6 −8

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ tx2gene <- function(organism){

		if(!file.exists(tx2gene_file)){
		tx2gene <- gtf("mouse") \|>
		as.data.table() \|>
		as.data.frame() \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")
		)
		@@ -34,17 +34,13 @@ dtu <- function(
		result_dir,
		organism = "mouse"
		){
		tx2gene <- tx2gene("mouse")
		tx2gene <- tx2gene(organism)

		if(is.na(names(ctl_count_files))){
		names(ctl_count_files) <- gsub("/quant.sf","",ctl_count_files) \|>
		basename()
		}

		if(is.na(names(obs_count_files))){
		names(obs_count_files) <- gsub("/quant.sf","",obs_count_files) \|>
		basename()
		}

		cts <- c(ctl_count_files,obs_count_files) \|>
		import_counts(
		@@ -56,8 +52,10 @@ dtu <- function(

		pd <- data.frame(
		id = colnames(cts),
		group = sub_dt[,samples],
		stringsAsFactors = FALSE
		group = c(
		rep(ctl_name,length(ctl_count_files)),
		rep(obs_name,length(obs_count_files))
		)
		)

		dturtle <- cts \|>