modified RNA-seq.R in R (ef54e49b) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+13 −3

Original line number	Diff line number	Diff line
		@@ -105,8 +105,9 @@ c.rnaseq <- function(

		}

		if(is.null(dge_list)){
		ct <- tolower(count_type)

		if(is.null(dge_list)){
		if(ct == "star"){
		cols <- c(1, 2)
		header_str <- FALSE
		@@ -119,6 +120,10 @@ c.rnaseq <- function(
		cols <- c(1,5)
		header_str <- TRUE
		skip_rows <- 0
		}else if(ct == "tcga"){
		cols <- c(1,4)
		header_str <- FALSE
		skip_rows <- 6
		}

		x <- readDGE(
		@@ -134,16 +139,21 @@ c.rnaseq <- function(
		x$samples$group <- group

		if(is.null(gtf_dt)){
		if(count_type %in% c("star","featurecounts")){
		if(ct %in% c("star","featurecounts")){
		gtf_dt <- c.gtf(organism,"gene") %>%
		as.data.table() %>%
		.[,.(gene_id,gene_name,type = gene_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}else if(count_type == "salmon"){
		}else if(ct == "salmon"){
		gtf_dt <- c.gtf(organism,"transcript") %>%
		as.data.table() %>%
		.[,.(gene_id = transcript_id,gene_name = transcript_name,type = transcript_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}else if(ct == "tcga"){
		gtf_dt <- lapply(dir(),\(x){fread(x)[!1:4,.(gene_id,gene_name,type = gene_type)]}) \|>
		rbindlist() \|>
		unique() \|>
		setkey(gene_id,gene_name)
		}
		}