From 7bd0fd6d86db897fe91414edb672c7e811a8e1db Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 20 Feb 2025 13:06:38 +0300
Subject: refactor: Use p=0.63 in permutation summary for suggestive threshold.

---
 scripts/rqtl2_wrapper.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'scripts/rqtl2_wrapper.R')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index 7cad7d5..52a37be 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -434,7 +434,7 @@ get_lod_significance <- function(perm, threshold = c(0.01, 0.05)){
      summary(perm, alpha = threshold)
 }
 
-lod_significance <- get_lod_significance(perm, threshold =c(0.33, 0.05, 0.01))
+lod_significance <- get_lod_significance(perm, threshold =c(0.63, 0.05, 0.01))
 permutation_results_file = file.path(opt$directory, "permutation.csv")
 significance_results_file = file.path(opt$directory, "significance.csv")
 write.csv(lod_significance, significance_results_file)
-- 
cgit 1.4.1