From fe1e3b600511ceedbd6778618d2c0d7e9ea2ffb6 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Fri, 25 Oct 2024 16:51:55 +0300
Subject: feat: add function to fetch load peaks for 1 QTL.

---
 scripts/rqtl2_wrapper.R | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

(limited to 'scripts')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index babf19e..cbf2b93 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -315,7 +315,7 @@ perform_permutation_test <- function(cross,
   }
   else if (method == "LOCO") {
     kinship = calc_kinship(genome_prob, "loco")
-    operm3 <- scan1perm(
+    perm <- scan1perm(
       genome_prob,
       cross$pheno,
       kinship = kinship ,
@@ -331,3 +331,22 @@ perform_permutation_test <- function(cross,
 perm <- perform_permutation_test(dataset, Pr, n_perm = 2, method = "LMM")
 # get the permutation summary with a significance threshold
 summary(perm, alpha = c(0.2, 0.05))
+
+# find function to perform the LOD peaks
+
+find_lod_peaks <-function(scan_results, cross, threshold=4,  drop=1.5){
+# can this take pmap??? which map should we use???
+# TODO add more ags
+print("Finding the lod peaks with thresholds n and drop n\n")
+return (find_peaks(scan_results, cross$gmap, threshold= threshold, drop=drop))
+}
+
+# add the number of cores
+lod_peaks <- find_lod_peaks(results, dataset)
+print(load_peaks)
+
+# how can we perform qtl effect computations ??? with input from user
+
+# what data should we return to the user
+
+# improve on this script
\ No newline at end of file
-- 
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