DeBUG taxa index and GTindex

jiabowang · May 8, 2024 · 8d6651c · 8d6651c
1 parent 4e8702e
commit 8d6651c
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/R/GAPIT.EMMAxP3D.R b/R/GAPIT.EMMAxP3D.R
@@ -421,7 +421,8 @@
             } 
             m <- ncol(xs) #number of SNPs
             t <- nrow(xs) #number of individuals
-
+            # print(m)
+            # print(t)
             Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before cleaning")
             Memory=GAPIT.Memory(Memory=Memory,Infor="Before cleaning")
   #allocate spaces for SNPs
@@ -620,6 +621,7 @@
           #if(i == 1) {print("the head of X for running GWAS is")}
           #if(i == 1) {print(head(X))}
                        }
+                       # print(X)
                      } #end of i >0 | file>file.from|frag>1
        #Recalculate eig and REML if not using P3D  NOTE THIS USED TO BE BEFORE the two solid lines
                      if(SNP.P3D==FALSE & !is.null(K))
@@ -759,7 +761,9 @@
                      }
 
                      beta <- crossprod(iXX,XY) #Note: we can use crossprod here becase iXX is symmetric
-
+                     # print(iXX)
+                     # print(XY)
+                     # print(beta)
 #--------------------------------------------------------------------------------------------------------------------<
                      if(i ==0 &file==file.from &frag==1)
                      { 

diff --git a/R/GAPIT.HapMap.R b/R/GAPIT.HapMap.R
@@ -29,7 +29,8 @@ function(G,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator =
     #print(paste("Number of bits for genotype: ", bit))
 
     print("Perform numericalization")
-
+    # Gtest=G[-1,-(1:11)]
+    # print(Gtest[1:5,1:6])
     if(heading){
         if(!Create.indicator) GD= apply(G[-1,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
         if(Create.indicator) GD= t(G[-1,-(1:11)])
@@ -43,9 +44,7 @@ function(G,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator =
         GT=NULL
         GI=NULL
     }
-
-    #print("The dimension of GD is:")
-    #print(dim(GD))
+    # print(GD[1:6,1:5])
 
 
     if(!Create.indicator) {print(paste("Succesfuly finished converting HapMap which has bits of ", bit,sep="")) }

diff --git a/R/GAPIT.Main.R b/R/GAPIT.Main.R
@@ -692,7 +692,7 @@ function(Y,
 #Z1=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
                   Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Prio PreP3D")
                   Memory=GAPIT.Memory(Memory=Memory,Infor="Prio PreP3D")  
-                # print(optOnly)   
+                # print(colInclude)   
                 # print(head(CVI))           
                   p3d <- GAPIT.EMMAxP3D(ys=ys,
                                       xs=as.matrix(as.data.frame(GD[,colInclude])),

diff --git a/R/GAPIT.Numericalization.R b/R/GAPIT.Numericalization.R
@@ -114,27 +114,27 @@ position=order(count)
 if(bit==1){
   lev0=c("R","Y","S","W","K","M") 
   inter=intersect(lev,lev0)
-}else{
-  inter=lev
-}
+}#else{
+  #inter=lev
+#}#
 
 #1status other than 2 or 3
 if(len<=1 | len> 3)x=0
 
 #2 status
 if(len==2)
 {
-
   if(!setequal(character(0),inter))
   {
     x=ifelse(x=="N",NA,ifelse(x==inter,1,0)) 
-    }else{
+  }else{
     x=ifelse(x=="N",NA,ifelse(x==lev[1],0,2))     # the most is set 0, the least is set 2
   }
 }
 
 #3 status
-if(bit==1){
+if(bit==1)
+{
 	if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[1],0,ifelse(x==lev[3],1,2)))
 }else{
 	if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[lev!=inter][1],0,ifelse(x==inter,1,2)))