From 038b3cd1416d406ae8a55948795c93a3106b4acc Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Mon, 11 Nov 2024 11:38:34 +0300
Subject: feat: implementation for getting meffects for multiparent population.

---
 scripts/rqtl2_wrapper.R | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

(limited to 'scripts')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index c3f6932..a4fcbfb 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -496,18 +496,17 @@ covar  <- NULL
 covar
 
 
-
-# TODO fix this hardcoded chromosome
-# TODO get all chromosomes and iterate coeff_results for a given chromosomes
-coeff_results  <- get_qtl_effect("5", Pr, pheno)
-
 meffects <- c()
 # TODO add plots for meffects
-
 for (chr in chr_names(dataset)){
   cat("Getting the qtl effect for chromosome", chr)
   cat("\n")
-   coeff_results  <- get_qtl_effect(chr, Pr, pheno)
+   if (dataset$crosstype == "4way"){
+     coeff_results <- get_qtl_effect(chr, aPr, pheno, LOCO="LOCO", covar = sex)
+   } else {
+    coeff_results  <- get_qtl_effect(chr, Pr, pheno)
+   }
+
     meffects <- append(meffects, coeff_results)
 }
 
-- 
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