DeBUG with BLUE in I and N

jiabowang · Apr 11, 2024 · cd01e77 · cd01e77
1 parent f708935
commit cd01e77
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/R/GAPIT.Main.R b/R/GAPIT.Main.R
@@ -1407,7 +1407,7 @@ if((!byPass)&(!Model.selection)){
  print("GAPIT before BLUP and BLUE")
  #print(dim(p3d$BLUE))
  BLUE=data.frame(cbind(data.frame(CV.taxa),data.frame(p3d$BLUE)))
- print(head(BLUE))
+ # print(head(BLUE))
  colnames(BLUE)=c("Taxa","BLUE.N","BLUE.I")
  QTNs=rep(0,nrow(BLUE))
  #Initial BLUP as BLUe and add additional columns

diff --git a/R/GAPIT.SS.R b/R/GAPIT.SS.R
@@ -55,9 +55,14 @@ if(DP$SNP.test)
 				        DPP=DP$DPP,file.output=DP$file.output,Multi_iter=DP$Multi_iter,num_regwas=DP$num_regwas )
      GWAS=myBus$GWAS
      Pred=myBus$Pred
-
+     p=GWAS[,4]
+     # print(head(GWAS))
+     # print(head(ic_GM))
+     myBus$seqQTN=match(as.character(GWAS[p<(DP$cutOff/length(p)),1]),as.character(ic_GM[,1]))
+     myBus$seqQTN=myBus$seqQTN[!is.na(myBus$seqQTN)]
  # BUS Prediction with gBLUP
 # lmpred=TRUE
+
      print(myBus$seqQTN)
      if(buspred)
      {  
@@ -207,7 +212,8 @@ if(DP$SNP.test)
           }
           # cv.licols=GAPIT.Licols(X=busCV[,-1])
           # geneGD=cv.licols$Xsub
-          # print(table(cv.licols$idx))
+          # print(dim(busCV))
+          # print(head(busCV))
           # busCV=as.data.frame(busCV[,cv.licols$idx])
           busCV=cbind(as.data.frame(busCV[,1]),matrix(as.numeric(as.matrix(busCV[,-1])),nrow(busCV),ncol(busCV)-1))
 

diff --git a/R/GAPIT.SUPER.GS.R b/R/GAPIT.SUPER.GS.R
@@ -506,14 +506,14 @@ if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
   X.idx=XX$idx
   if (is.null(Z)) Z=diag(x=1,nrow(K),ncol(K))
 
-  # print(my_allCV)
+  # print(head(X))
 
    emma_REMLE <- EMMREML::emmreml(y=as.numeric(ys), X=as.matrix(X), K=as.matrix(K), Z=Z,varbetahat=TRUE,varuhat=TRUE, PEVuhat=TRUE, test=TRUE)  
   }else{
    emma_REMLE=emma_test
    print("gBLUP with only one time emma")
   } 
-  # print(dim(X))
+  # print(dim(my_allCV))
 
   if (is.null(my_allCV))
   {
@@ -534,13 +534,13 @@ if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
     beta.I=emma_REMLE$betahat[c((2+CV.Extragenetic):(ncol(XCV)-QTN.gs))]
     beta.N=emma_REMLE$betahat[c(1:(1+CV.Extragenetic))]
     if(QTN.gs!=0)beta.QTN=emma_REMLE$betahat[c((ncol(XCV)-QTN.gs):ncol(XCV))]
-    # print(dim(XCVN))
-    # print(length(beta.N))
+    # print(dim(XCVI))
+    # print(length(beta.I))
     BLUE.N=XCVN%*%beta.N
     BLUE.QTN=rep(0,length(BLUE.N))    
     if(QTN.gs!=0)BLUE.QTN=XCVqtn%*%beta.QTN
     BLUE.I=rep(0,length(BLUE.N))
-    if(CV.Extragenetic!=0)BLUE.I=XCVI%*%beta.I
+    if(CV.Extragenetic!=(ncol(XCV)))BLUE.I=XCVI%*%beta.I
     #Interception only
    # print(dim(my_allX))
    # print(length(emma_REMLE$betahat))