modified dturtle.R in R (2007c727) · Commits · Chaos / chaos.tools

R/dturtle.R

+12 −8

Original line number	Diff line number	Diff line
		@@ -28,12 +28,14 @@ tx2gene <- function(organism){

		dtu <- function(
		ctl_count_files,
		ctl_name,
		ctl,
		obs_count_files,
		obs_name,
		obs,
		result_dir,
		organism = "mouse"
		){
		biocpar <- BiocParallel::MulticoreParam(getDTthreads())

		tx2gene <- tx2gene(organism)

		names(ctl_count_files) <- gsub("/quant.sf","",ctl_count_files) \|>
		@@ -53,18 +55,18 @@ dtu <- function(
		pd <- data.frame(
		id = colnames(cts),
		group = c(
		rep(ctl_name,length(ctl_count_files)),
		rep(obs_name,length(obs_count_files))
		rep(ctl,length(ctl_count_files)),
		rep(obs,length(obs_count_files))
		)
		)

		dturtle <- cts \|>
		run_drimseq(
		tx2gene = tx2gene,
		tx2gene = data.frame(tx2gene),
		pd = pd,
		id_col = "id",
		cond_col = "group",
		cond_levels = c(obs_name,ctl_name),
		cond_levels = c(obs,ctl),
		filtering_strategy = "bulk",
		BPPARAM = biocpar
		) \|>
		@@ -73,7 +75,7 @@ dtu <- function(
		posthoc = 0.1
		)

		dturtle$dge_analysis <- files \|>
		dturtle$dge_analysis <- c(ctl_count_files,obs_count_files) \|>
		import_dge_counts(
		type = "salmon",
		tx2gene = tx2gene[,c("transcript_id", "gene_name")]
		@@ -82,7 +84,7 @@ dtu <- function(
		pd = pd,
		id_col = "id",
		cond_col = "group",
		cond_levels = c(obs_name,ctl_name),
		cond_levels = c(obs,ctl),
		lfc_threshold = 0.5,
		sig_threshold = 0.01,
		dge_calling_strategy = "bulk",
		@@ -99,4 +101,6 @@ dtu <- function(
		add_gene_metadata = list("chromosome"="seqnames"),
		add_tx_metadata = list("tx_expr_in_max" = c("exp_in", max))
		)

		dturtle
		}
		No newline at end of file