modified gtf.R added dturtle.R (f7c29c93) · Commits · Chaos / chaos.tools

R/dturtle.R

0 → 100644

+100 −0

Original line number	Diff line number	Diff line
		tx2gene <- function(organism){
		tx2gene_file <- file.path(
		chaos_info("data_dir"),
		paste0("tx2gene_for_dturtle",organism,"rds",sep = ".")
		)

		if(!file.exists(tx2_gene_file)){
		tx2gene <- gtf("mouse") \|>
		as.data.table() \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")
		)

		tx2gene$gene_name <- one_to_one_mapping(
		name = tx2gene$gene_name,
		id = tx2gene$gene_id
		)
		tx2gene$transcript_name <- one_to_one_mapping(
		name = tx2gene$transcript_name,
		id = tx2gene$transcript_id
		)
		saveRDS(tx2gene,tx2gene_file,compress = "xz")
		}else{
		tx2gene <- readRDS(tx2gene_file)
		}
		tx2gene
		}

		dtu <- function(
		ctl_count_file,
		ctl_name,
		obs_count_file,
		obs_name,
		result_dir,
		organism = "mouse"
		){
		tx2gene <- tx2gene("mouse")

		names(ctl_count_file) <- gsub("/quant.sf","",ctl_count_file) \|>
		basename()

		names(obs_count_files) <- gsub("/quant.sf","",ctl_count_file) \|>
		basename()

		cts <- c(ctl_count_files,obs_count_files) \|>
		import_counts(
		type = "salmon",
		tx2gene = tx2gene[,c("transcript_id", "gene_name")]
		)

		rownames(cts) <- tx2gene$transcript_name[match(rownames(cts), tx2gene$transcript_id)]

		pd <- data.frame(
		id = colnames(cts),
		group = sub_dt[,samples],
		stringsAsFactors = FALSE
		)

		dturtle <- cts \|>
		run_drimseq(
		tx2gene = tx2gene,
		pd = pd,
		id_col = "id",
		cond_col = "group",
		cond_levels = c(obs_name,ctl_name),
		filtering_strategy = "bulk",
		BPPARAM = biocpar
		) \|>
		posthoc_and_stager(
		ofdr = 0.05,
		posthoc = 0.1
		)

		dturtle$dge_analysis <- files \|>
		import_dge_counts(
		type = "salmon",
		tx2gene = tx2gene[,c("transcript_id", "gene_name")]
		) \|>
		run_deseq2(
		pd = pd,
		id_col = "id",
		cond_col = "group",
		cond_levels = c(obs_name,ctl_name),
		lfc_threshold = 0.5,
		sig_threshold = 0.01,
		dge_calling_strategy = "bulk",
		BPPARAM = biocpar
		)

		dtu_dge_genes <- intersect(
		dturtle$sig_gene,
		dturtle$dge_analysis$results_sig$gene
		)

		dturtle <- create_dtu_table(
		dturtle = dturtle,
		add_gene_metadata = list("chromosome"="seqnames"),
		add_tx_metadata = list("tx_expr_in_max" = c("exp_in", max))
		)
		}
		No newline at end of file

R/gtf.R

+0 −24

Original line number	Diff line number	Diff line
		@@ -91,27 +91,3 @@ txdb <- function(
		txdb
		}
		}

		tx2gene <- function(organism){
		tx2gene_file <- file.path(dir,paste0("tx2gene_for_dturtle",organism,"rds",sep = "."))
		if(!file.exists(tx2_gene_file)){
		tx2gene <- gtf("mouse") \|>
		as.data.table() \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")
		)

		tx2gene$gene_name <- one_to_one_mapping(
		name = tx2gene$gene_name,
		id = tx2gene$gene_id
		)
		tx2gene$transcript_name <- one_to_one_mapping(
		name = tx2gene$transcript_name,
		id = tx2gene$transcript_id
		)
		saveRDS(tx2gene,tx2gene_file,compress = "xz")
		}else{
		tx2gene <- readRDS(tx2gene_file)
		}
		tx2gene
		}
		No newline at end of file

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