From 8981ef0585dd6b74b6719faa886d0c9880f18698 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 13 Oct 2021 14:36:34 +0300
Subject: get significant interactions

---
 scripts/ctl_analysis.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R
index 04b55f9..6c3b22f 100644
--- a/scripts/ctl_analysis.R
+++ b/scripts/ctl_analysis.R
@@ -1,6 +1,8 @@
 library(ctl)
 
 # The genotypes.csv file containing the genotype matrix is stored individuals (rows) x genetic marker (columns):
+
+
 genotypes <- read.csv("genotypes.csv",row.names=1, header=FALSE, sep="\t")
 # The phenotypes.csv file containing individuals (rows) x traits (columns) measurements:
 traits <- read.csv("phenotypes.csv",row.names=1, header=FALSE, sep="\t")
@@ -11,6 +13,7 @@ ctls <- CTLscan(geno,traits,strategy=input$strategy,
 	nthreads=6,verbose=TRUE)
 
 
-# plots and ctl networks
 
+#output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
+sign <- CTLsignificant(ctls,significance = input$significance)
 
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