From 95ca78a638a7f01788f8ecea63c4917a465ff2e0 Mon Sep 17 00:00:00 2001
From: jiabowang <jiabowangyifeng@gmail.com>
Date: Tue, 12 Dec 2023 10:59:07 +0800
Subject: [PATCH] Avoid rare frequency genotype in the Random model

---
 R/GAPIT.Numericalization.R | 16 +++-------------
 R/GAPIT.R                  |  1 +
 R/GAPIT.RandomModel.R      |  4 ++++
 3 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/R/GAPIT.Numericalization.R b/R/GAPIT.Numericalization.R
index f6beb0d..5d23c71 100644
--- a/R/GAPIT.Numericalization.R
+++ b/R/GAPIT.Numericalization.R
@@ -66,7 +66,9 @@ for(i in 1:len){
 	count[i]=length(x[(x==lev[i])])
 }
 
-#print(count)
+# print(count)
+# print(len)
+# print()
 
 if(Major.allele.zero){
   if(len>1 & len<=3){
@@ -108,18 +110,6 @@ position=order(count)
 
 #Jiabo creat this code to convert AT TA to 1 and 2.2018.5.29
 
-# lev1=lev
-# if(bit==2&len==3) 
-# {
-# lev1[1]=lev[count==sort(count)[1]]
-# lev1[2]=lev[count==sort(count)[2]]
-# lev1[3]=lev[count==sort(count)[3]]
-# position=c(1:3)
-# lev=lev1
-# }
-#print(lev)
-#print(position)
-#print(inter)
 #Jiabo code is end here
 if(bit==1){
   lev0=c("R","Y","S","W","K","M") 
diff --git a/R/GAPIT.R b/R/GAPIT.R
index e581372..e609cc0 100644
--- a/R/GAPIT.R
+++ b/R/GAPIT.R
@@ -512,6 +512,7 @@ if(!is.null(Y))
             out=c(out,myG_simulation)
             if(file.output)ViewPhenotype<-GAPIT.Phenotype.View(myY=myG_simulation$Y,traitname="Simulated.Phenotype",memo=memo0)
           }
+        print("Now the GAPIT is cbind taxa and numeric genotype...")
         out$GD=data.frame(cbind(as.data.frame(GT),as.data.frame(GD)))
         out$GM=GI
         out$G=myGenotype$G
diff --git a/R/GAPIT.RandomModel.R b/R/GAPIT.RandomModel.R
index 7c4a275..1a5bda1 100644
--- a/R/GAPIT.RandomModel.R
+++ b/R/GAPIT.RandomModel.R
@@ -33,6 +33,10 @@ function(GWAS,Y,CV=NULL,X,cutOff=0.01,GT=NULL,name.of.trait=NULL,N.sig=NULL,n_ra
     }
     geneGD=X[,index,drop=FALSE]
     geneGWAS=GWAS[index,,drop=FALSE]
+    var.gd=diag(var(geneGD))
+    var.index=var.gd>0.0001
+    geneGD=geneGD[,var.index]
+    geneGWAS=geneGWAS[var.index,]
     if(ld.cut)
     {
         gene.licols=GAPIT.Licols(X=geneGD)