modified RNA-seq.R in R (1c4091dd) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+15 −4

Original line number	Diff line number	Diff line
		@@ -7,13 +7,16 @@ rnaseq123 <- function(

		if(tolower(count_type) == "star"){
		cols <- c(1, 2)
		header_str <- TRUE
		header_str <- FALSE
		skip_rows <- 4
		}else if(tolower(count_type) == "featurecounts")
		{
		}else if(tolower(count_type) == "featurecounts"){
		cols <- c(1, 7)
		header_str <- FALSE
		skip_rows <- 1
		}else if(tolower(count_type) == "salmon"){
		cols <- c(1,5)
		header_str <- TRUE
		skip_rows <- 0
		}

		x <- readDGE(
		@@ -30,10 +33,18 @@ rnaseq123 <- function(

		x$samples$group <- group

		if(count_type %in% c("star","featurecounts")){
		gtf_info <- gtf(organism,"gene") %>%
		as.data.table() %>%
		.[,.(gene_id,gene_name,type,chr = seqnames,start,end,strand)] \|>
		.[,.(gene_id,gene_name,type = gene_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}else if(count_type == "salmon"){
		gtf_info <- 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)
		}


		## it will take few minutes to load the gtf_file
		## filter the unneeded rows