modified gtf.R in R (54b95e72) · Commits · Chaos / chaos.tools

R/gtf.R

+4 −4

Original line number	Diff line number	Diff line
		c.anno <- function(organism,type = NA){
		if(organism == "human"){
		info <- c(ref = "hg38", anno_v = "v42")
		info <- c(ref = "hg38", anno_v = "gencode.v42")
		}else if(organism == "mouse"){
		info <- c(ref = "mm39", anno_v = "vM31")
		info <- c(ref = "mm39", anno_v = "gencode.vM31")
		}
		if(is.na(type)){
		info
		@@ -21,7 +21,7 @@ c.gtf <- function(
		gtf_file <- paste0(
		"~/Reference/",
		ref,
		"/annotation/gencode.",
		"/annotation/",
		anno_v,
		".annotation.gtf.gz"
		)
		@@ -38,7 +38,7 @@ c.gtf <- function(
		c.info("data_dir"),
		"/",
		ref,
		".gencode.",
		".",
		anno_v,
		".annotation.gtf",
		type_str