modified gtf.R in R (4018f288) · Commits · Chaos / chaos.tools

R/gtf.R

+3 −3

Original line number	Diff line number	Diff line
		@@ -70,11 +70,11 @@ txdb <- function(
		)

		if(file.exists(txdb_file)){
		AnnotationDbi::loadDb(txdb_file)
		loadDb(txdb_file)
		}else{
		chaos_info("data_dir") \|> chaos_create_dir()
		txdb <- gtf_file \|>
		GenomicFeatures::makeTxDbFromGFF(
		makeTxDbFromGFF(
		dataSource = base_name(gtf_file,"annotation.gtf") %>% gsub(".gz","",.),
		organism = organism,
		chrominfo = chr_size(
		@@ -84,7 +84,7 @@ txdb <- function(
		)[,.(chrom = chr,length,genome = name)]
		)

		AnnotationDb::saveDb(txdb,txdb_file)
		saveDb(txdb,txdb_file)

		txdb
		}