update gtf in other functions (77831e62) · Commits · Chaos / chaos.tools

R/dtu_analysis.R

+2 −3

Original line number	Diff line number	Diff line
		@@ -3,8 +3,7 @@ dtu_analysis <- function(
		obs_files,
		ctl,
		obs,
		ref,
		anno_v,
		organism,
		out_dir = NA,
		fdr = 0.05,
		post_threashold = 0.1,
		@@ -18,7 +17,7 @@ dtu_analysis <- function(

		if(!dir.exists(out_dir)){dir.create(out_dir)}

		tx2gene <- gtf(ref,anno_v,"transcript") \|>
		tx2gene <- gtf(organism,"transcript") \|>
		move_columns_to_front(
		columns = c("transcript_name", "gene_name")
		)

+4 −6

Original line number	Diff line number	Diff line
		@@ -113,9 +113,8 @@ juicer_eigen <- function(
		resolution = 25e4,
		chr_list = NA,
		norm = "KR",
		ref = "hg19",
		juicer_tool_path = "~/local/chaos.juicer/common/feature_tools.jar",
		annotation = "~/Data/Reference/hg19/annotation/gencode.v38lift37.annotation.gff3.gz"
		organism,
		juicer_tool_path = "~/local/chaos.juicer/common/feature_tools.jar"
		){
		chr_list <- chr_list(
		hic_file = hic_file,
		@@ -140,9 +139,8 @@ juicer_eigen <- function(
		rbindlist()

		gd <- gene_density(
		ref = ref,
		resolution = resolution,
		annotation = annotation
		organism = organism,
		resolution = resolution
		)[
		chr %in% c(chr_list, paste0("chr",chr_list)),
		.(chr,start,end,gene_number)