From 006f3f73c20431754b8b6e5c2fc50202b2b7d926 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Mon, 11 Nov 2024 12:07:45 +0300
Subject: refactor: adding pseudomarkers o genetic probabilites map.

---
 scripts/rqtl2_wrapper.R | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

(limited to 'scripts/rqtl2_wrapper.R')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index 6581ed4..d025935 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -178,16 +178,13 @@ perform_genetic_pr <- function(cross,
 
   cat("Finding the  genetic Probabilities\n")
   if (use_pseudomarkers){
+  cat("Using pseudo markers for genetic probabilites\n")
   map <- insert_pseudomarkers(cross$gmap, step=step)
+  }
   return(calc_genoprob(cross, map=map,
                        error_prob=error_prob, map_function=map_function,
-		       quiet=FALSE, cores=cores))
-  }
-  else {
-      return (calc_genoprob(cross, map=map, error_prob=error_prob,
-                           quiet = FALSE, map_function =map_function,
-                           cores = cores))
-  }}
+		       quiet=FALSE, cores=cores)) 
+}
 
 Pr = perform_genetic_pr(dataset)
 cat("Summaries  on the genetic probabilites \n")
-- 
cgit 1.4.1