update gtf in other functions (69c9cc58) · Commits · Chaos / chaos.tools

R/juicer_tool.R

+3 −5

Original line number	Diff line number	Diff line
		@@ -278,9 +278,8 @@ eigen_switch <- function(
		obs = "DMSO_DHT.hic",
		chr_list = NA,
		resolution = 25e4,
		ref = "hg19",
		organism,
		juicer_tool_path = "~/local/chaos.juicer/common/feature_tools.jar",
		annotation = "~/Data/Reference/hg19/annotation/gencode.v38lift37.annotation.gff3.gz",
		correction = TRUE
		){
		# chr_list <- chr_list(
		@@ -297,11 +296,10 @@ eigen_switch <- function(
		function(x){
		dt <- juicer_eigen(
		hic_file = x[2],
		ref = ref,
		organism = organism,
		chr_list = chr_list,
		resolution = resolution,
		juicer_tool_path = juicer_tool_path,
		annotation = annotation
		juicer_tool_path = juicer_tool_path
		)[
		,No := 1:.N,
		.(chr)