add matching taxa of KI in IC

R/GAPIT.Blink.R

@@ -335,6 +335,7 @@
       P[P==0] <- min(P[P!=0],na.rm=TRUE)*0.01
       P[is.na(P)] =1
       # print(str(myGLM))
+
       gc()
       nf=ncol(myGLM$P)/4
       tvalue=myGLM$P[,nf*2-shift]

R/GAPIT.Genotype.R

@@ -115,8 +115,8 @@ if(!needKinPC &SNP.fraction<1)  stop("GAPIT says: You did not require calculate
 if(!SNP.test & is.null(KI) & !byData & !byFile)  stop("GAPIT says: For SNP.test optioin, please input either use KI or use genotype")
 
 #if(is.null(file.path) & !byData & byFile) stop("GAPIT Ssays: A path for genotype data should be provided!")
-if(is.null(file.total) & !byData & byFile) stop("GAPIT Ssays: Number of file should be provided: >=1")
-if(!is.null(G) & !is.null(GD)) stop("GAPIT Ssays: Both hapmap and EMMA format exist, choose one only.")
+if(is.null(file.total) & !byData & byFile) stop("GAPIT Says: Number of file should be provided: >=1")
+if(!is.null(G) & !is.null(GD)) stop("GAPIT Says: Both hapmap and EMMA format exist, choose one only.")
 
 if(!is.null(file.GD) & is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
 if(is.null(file.GD) & !is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")

R/GAPIT.Genotype.View.R

@@ -1,5 +1,5 @@
 `GAPIT.Genotype.View` <-function(GI=NULL,X=NULL,chr=NULL, 
-                                 WS0=NULL,ws=200,Aver.Dis=1000,...){
+                                 WS0=NULL,ws=20,Aver.Dis=1000,...){
 # Object: Analysis for Genotype data:Distribution of SNP density,Accumulation,Moving Average of density,result:a pdf of the scree plot
 # myG:Genotype data
 # chr: chromosome value
@@ -132,9 +132,22 @@ for(i in 1:length(chr))
 }
 odd=seq(1,length(chr),2)
 r=mapply(GAPIT.Cor.matrix,as.data.frame(x1),as.data.frame(x2))
+d.V=dist/Aver.Dis
+
+# fig.d=cbind(d.V[rs.index],(r^2)[rs.index])
+# dv=d.V[rs.index]
+# r2=(r^2)[rs.index]
+# dv2=ceiling(dv/ws)*ws
+# dv2.un=as.character(unique(dv2))
+# fig.d=NULL
+# for(i in 1:length(dv2.un))
+# {
+#   index=dv2==dv2.un[i]
+#   fig.d=rbind(fig.d,cbind(dv2.un[i],mean(r2[index],na.rm=TRUE)))
+# }
+
 
 grDevices::pdf("GAPIT.Genotype.Density_R_sqaure.pdf", width =10, height = 6)
-d.V=dist/Aver.Dis
 # print(summary(d.V))
 par(mfcol=c(2,3),mar = c(5,5,2,2))
 plot(r[rs.index], xlab="Marker",las=1,xlim=c(1,mm), 
@@ -171,6 +184,7 @@ d.V.hist$counts=d.V0/d.V0.demo
 plot(d.V[rs.index],r[rs.index], las=1,xlab="Distance (Kb)", ylab="R", main="c",cex=.5,col="gray60",xlim=c(0,WS0/Aver.Dis))
 abline(h=0,col="darkred")
 plot(d.V[rs.index],(r^2)[rs.index], las=1,xlab="Distance (Kb)", ylab="R sqaure", main="d",cex=.5,col="gray60",xlim=c(0,WS0/Aver.Dis))
+# plot(as.numeric(fig.d[,1]),as.numeric(fig.d[,2]), las=1,xlab="Distance (Kb)", ylab="R sqaure", main="d",cex=.5,col="gray60",xlim=c(0,WS0/Aver.Dis))
 
 #Moving average
 dist2[dist2>WS0]=NA
@@ -181,7 +195,7 @@ maPure=ma[!indRM,]
 maPure=maPure[!is.na(maPure[,1]),]
 ns=nrow(maPure)
 # ws=ws
-slide=10
+slide=ws
 loc=matrix(NA,floor(ns/slide),2)
 
 for (i in 1:floor(ns/slide)){

R/GAPIT.IC.R

@@ -12,58 +12,68 @@ print("GAPIT.IC in process...")
      CV=DP$CV
      GD=DP$GD
      noCV=FALSE
-     if(is.null(CV)){
-     noCV=TRUE
-     if(is.null(GD))
+     if(is.null(CV))
      {
-       CV=Y[,1:2]
-          }else{
-       CV=GD[,1:2]
-     }
-     CV[,2]=1
-     colnames(CV)=c("taxa","overall")
-     print(paste("There is 0 Covarinces.",sep=""))
+       noCV=TRUE
+       if(is.null(GD))
+       {
+         CV=Y[,1:2]
+       }else{
+         CV=GD[,1:2]
+       }
+       CV[,2]=1
+       colnames(CV)=c("taxa","overall")
+       print(paste("There is 0 Covarinces.",sep=""))
      }
      Y=Y[!is.na(Y[,2]),]
      taxa_Y=as.character(Y[,1])
      # print(head(Y))
      if(DP$PCA.total>0&!is.null(DP$CV))CV=GAPIT.CVMergePC(DP$CV,PC)
      if(DP$PCA.total>0&is.null(DP$CV))CV=PC
-     if(is.null(GD)&!is.null(DP$KI))
+     if(!is.null(GD))
      {
-     taxa_KI=as.character(DP$KI[,1])
-     taxa_CV=as.character(CV[,1])
-     taxa_comall=intersect(intersect(taxa_KI,taxa_Y),taxa_CV)
+       if(!is.null(DP$KI))
+       {
+         taxa_GD=as.character(GD[,1])
+         taxa_KI=as.character(DP$KI[,1])
+         taxa_CV=as.character(CV[,1])
+         taxa_comall=intersect(intersect(intersect(taxa_KI,taxa_GD),taxa_Y),taxa_CV)
      # print(length(taxa_comall))
-     comCV=CV[taxa_CV%in%taxa_comall,]
-     comCV <- comCV[match(taxa_comall,as.character(comCV[,1])),]
-     comY=Y[taxa_Y%in%taxa_comall,]
-     comY <- comY[match(taxa_comall,as.character(comY[,1])),]
-
-     comGD=NULL
+         comCV=CV[taxa_CV%in%taxa_comall,]
+         comCV <- comCV[match(taxa_comall,as.character(comCV[,1])),]
+         comY=Y[taxa_Y%in%taxa_comall,]
+         comY <- comY[match(taxa_comall,as.character(comY[,1])),]
+         comGD=GD[taxa_GD%in%taxa_comall,]
+         comGD <- comGD[match(taxa_comall,as.character(comGD[,1])),]# comGD=NULL
 
-     }else{
+       }else{
      # print("@@@@")
-     taxa_GD=as.character(GD[,1])
-     taxa_comGD=as.character(GD[,1])
-     taxa_CV=as.character(CV[,1])
-     taxa_comall=intersect(intersect(taxa_GD,taxa_Y),taxa_CV)
-     comCV=CV[taxa_CV%in%taxa_comall,]
-     comCV <- comCV[match(taxa_comall,as.character(comCV[,1])),]
-
-     comGD=GD[taxa_GD%in%taxa_comall,]
-     comGD <- comGD[match(taxa_comall,as.character(comGD[,1])),]
-
-     comY=Y[taxa_Y%in%taxa_comall,]
-     comY <- comY[match(taxa_comall,as.character(comY[,1])),]
+         taxa_GD=as.character(GD[,1])
+         taxa_comGD=as.character(GD[,1])
+         taxa_CV=as.character(CV[,1])
+         taxa_comall=intersect(intersect(taxa_GD,taxa_Y),taxa_CV)
+         comCV=CV[taxa_CV%in%taxa_comall,]
+         comCV <- comCV[match(taxa_comall,as.character(comCV[,1])),]
+         comGD=GD[taxa_GD%in%taxa_comall,]
+         comGD <- comGD[match(taxa_comall,as.character(comGD[,1])),]
+         comY=Y[taxa_Y%in%taxa_comall,]
+         comY <- comY[match(taxa_comall,as.character(comY[,1])),]
+       }
+     }else{
+       # taxa_GD=as.character(GD[,1])
+       taxa_KI=as.character(DP$KI[,1])
+       taxa_CV=as.character(CV[,1])
+       taxa_comall=intersect(intersect(taxa_KI,taxa_Y),taxa_CV)
+     # print(length(taxa_comall))
+       comCV=CV[taxa_CV%in%taxa_comall,]
+       comCV <- comCV[match(taxa_comall,as.character(comCV[,1])),]
+       comY=Y[taxa_Y%in%taxa_comall,]
+       comY <- comY[match(taxa_comall,as.character(comY[,1])),]
+       comGD=NULL
      }
-
-
      GT=as.matrix(as.character(taxa_comall))
      print(paste("There are ",length(GT)," common individuals in genotype , phenotype and CV files.",sep=""))
-
      if(nrow(comCV)!=length(GT))stop ("GAPIT says: The number of individuals in CV does not match to the number of individuals in genotype files.")
-
      print("The dimension of total CV is ")
      print(dim(comCV))
 

R/GAPIT.Main.R

@@ -425,11 +425,13 @@ function(Y,
 # print(length(GK))
     GTindex=match(as.character(KI[,1]),as.character(Y[,1]))
     GTindex=GTindex[!is.na(GTindex)]
-# KI=KI[GTindex,GTindex+1]
+    # KI=KI[GTindex,GTindex+1]
     my_taxa=as.character(KI[,1])
     CV=CV[as.character(CV[,1])%in%as.character(Y[,1]),]
-# print(dim(KI))
-# print(dim(CV))
+print(dim(KI))
+print(dim(CV))
+print(dim(Y))
+print(length(GTindex))
 
     #Output phenotype
     colnames(Y)=c("Taxa",name.of.trait)

R/GAPIT.RandomModel.R

@@ -29,16 +29,17 @@ function(GWAS,Y,CV=NULL,X,cutOff=0.01,GT=NULL,name.of.trait=NULL,N.sig=NULL,n_ra
     cutoff=max(sort.p[1:N.sig])
     index=P.value<=cutoff 
     }
-    geneGD=X[,index,drop=FALSE]
-    geneGWAS=GWAS[index,,drop=FALSE]
-    gene.licols=GAPIT.Licols(X=geneGD)
-    geneGD=gene.licols$Xsub
-    geneGWAS=geneGWAS[gene.licols$idx,]
+
     if(length(unique(index))==1)
     {
     	print("There is no significant marker for VE !!")
     	return(list(GVs=NULL))
     }
+    geneGD=X[,index,drop=FALSE]
+    geneGWAS=GWAS[index,,drop=FALSE]
+    gene.licols=GAPIT.Licols(X=geneGD)
+    geneGD=gene.licols$Xsub
+    geneGWAS=geneGWAS[gene.licols$idx,]
     index_T=as.matrix(table(index))
     # print(index_T)
     in_True=ncol(geneGD)