modified RNA-seq.R in R (35e05de8) · Commits · Chaos / chaos.tools

R/RNA-seq.R

+6 −1

Original line number	Diff line number	Diff line
		@@ -607,6 +607,7 @@ rnaseq123_multi <- function(
		group,
		compare,
		organism = "human",
		gtf_dt = NULL,
		count_type = "star"
		){
		if(is.null(dge_list)){
		@@ -636,6 +637,7 @@ rnaseq123_multi <- function(

		x$samples$group <- group

		if(is.null(gtf_dt)){
		if(count_type %in% c("star","featurecounts")){
		gtf_info <- gtf(organism,"gene") %>%
		as.data.table() %>%
		@@ -647,7 +649,10 @@ rnaseq123_multi <- function(
		.[,.(gene_id = transcript_id,gene_name = transcript_name,type = transcript_type,chr = seqnames,start,end,strand)] \|>
		setkey(gene_id,gene_name)
		}

		else if(file.exists(gtf)){
		gtf_info <- gtf_dt %>%
		setkey(gene_id,gene_name)
		}

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