From febd6ebebfba2b585d98c3e5e35c6713c9781036 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Fri, 7 Feb 2025 14:17:17 +0300
Subject: fix: pass the correct genome probabilites.

---
 scripts/rqtl2_wrapper.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'scripts/rqtl2_wrapper.R')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index 5ad812e..7cad7d5 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -226,9 +226,9 @@ print(Xcovar)
 #  Function to calculate the kinship 
 get_kinship <- function(probability, method="LMM"){
 if (opt$method == "LMM"){
-    kinship = calc_kinship(genome_prob)
+    kinship = calc_kinship(probability)
 } else if (opt$method == "LOCO"){
-    kinship = calc_kinship(genome_prob, "loco")
+    kinship = calc_kinship(probability, "loco")
 }else {
  kinship = NULL
 }
-- 
cgit 1.4.1