From e177ba8d9ad80261f980efca59a87aae2c0939c6 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Mon, 11 Nov 2024 10:27:05 +0300
Subject: feat: export chromosome names and qtl effects.

---
 scripts/rqtl2_wrapper.R | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index b68c82f..7bdc29a 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -467,16 +467,29 @@ 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)
+    meffects <- append(meffects, coeff_results)
+}
+
 output = list(lod_peaks = lod_peaks,
              scan_results =scan_results,
 	     genetic_probabilities = Pr,
 	     lod_significance = lod_significance,
 	     permutation_results = perm,
 	     lod_peaks = lod_peaks,
+	     chromosomes  = chr_names(dataset),
+	     meffects = meffects,
 	     lod_plot_path =lod_plot_path,
 	     scan_method = SCAN_METHOD  
 	     )
@@ -487,6 +500,3 @@ str_glue("The output file path is  {output_file_path}")
 cat("Writing to the output file\n")
 write(output_json_data, file=output_file_path)
 
-
-
-
-- 
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