First commit

R/CHEKALL.R

@@ -0,0 +1,155 @@
+
+chr<-unique(snp[,1])
+
+nc<-NULL
+for (i in 1:length(chr)){
+
+ nc[i]<-length(snp[which(snp[,1] %in% chr[i]),1])
+
+}
+
+
+chr<-unique(indel[,1])
+
+ncl<-NULL
+for (i in 1:length(chr)){
+
+ ncl[i]<-length(indel[which(indel[,1] %in% chr[i]),1])
+
+}
+
+snpname<-phased.maplist
+
+for (i in 1: length(snpname)){
+	snpname[[i]][,1]<-paste("LG",i,"_",paste("SNP",c(1:length(snpname[[i]][,1])),sep=""),sep="")
+}
+
+
+SNP_SSR<-list()
+
+for (i in 1:length(phased.maplist)){
+
+	SNP_SSR[[i]]<-ALL_dosages_a[which(phased.maplist[[i]][,1] %in% rownames(ALL_dosages_a)),]
+
+}
+
+
+capture.output(for (i in 0:45) for (j in 0:45) print(i/j),
+               file = "foo.txt")
+
+for (i in 1: length(SNP_SSR)){
+	rownames(SNP_SSR[[i]])<-paste("LG",i,"_",paste("SNP",c(1:length(rownames(SNP_SSR[[i]]))),sep=""),sep="")
+}
+
+N<-dim(SNPALL)[1]
+M<-dim(SNPALL)[1]
+
+
+for (i in 1: length(SNP_SSR)){
+	write.csv(SNP_SSR[[i]],file=paste("LGGEN",i,".csv",sep=""))
+	}
+
+
+
+nsnp<-NULL
+for (i in 1:length(phased.maplist)) {
+  nsnp[i]<-dim(phased.maplist[[i]])[1]
+}
+print(paste("Total Number of SNP Markers:",sum(nsnp)))
+
+
+nsnp<-NULL
+for (i in 1:length(phased.maplist_P1)) {
+  nsnp[i]<-dim(phased.maplist_P1[[i]])[1]
+}
+print(paste("Total Number of SNP Markers:",sum(nsnp)))
+
+nsnp<-NULL
+for (i in 1:length(phased.maplist_P2)) {
+  nsnp[i]<-dim(phased.maplist_P2[[i]])[1]
+}
+print(paste("Total Number of SNP Markers:",sum(nsnp)))
+
+
+
+##write the name and map
+
+load("polymap_tetra.RData")
+
+SNP_SSR<-list()
+
+for (i in 1:length(phased.maplist)){
+	SNP_SSR[[i]]<-ALL_dosages_a[match(phased.maplist[[i]][,1],rownames(ALL_dosages_a)),]
+
+
+}
+
+names(SNP_SSR)<-paste("LG",c(1:7),sep="")
+
+snpnameall<-phased.maplist
+
+for (i in 1: length(snpnameall)){
+	for (j in 1:length(snpnameall[[i]][,1])) {
+		if (is.na(match(snpnameall[[i]][j,1],rownames(polymap_tetra[[1]])))) {
+			next
+	} else {
+	new<-polymap_tetra[[2]][match(snpnameall[[i]][j,1],rownames(polymap_tetra[[1]])),]
+			rownames(SNP_SSR[[i]])[j]<-paste("c",new[,1],"_",new[,2],sep="")
+			snpnameall[[i]][j,1]<-paste("c",new[,1],"_",new[,2],sep="")
+	}
+	}
+	snpnameall[[i]][,1]<-rownames(SNP_SSR[[i]])
+}
+
+
+
+for (i in 1: length(SNP_SSR)){
+	write.csv(SNP_SSR[[i]],file=paste("LGGEN",i,".csv",sep=""))
+	}
+
+for (i in 1: length(SNP_SSR)){
+	SNP_SSR[[i]]<-paste("LG",i,sep="")
+	}
+
+
+
+SNP_SSR<-list()
+
+for (i in 1:length(phased.maplist)){
+	for (j in 1:length(phased.maplist[[i]][,1])){
+		SNP_SSR[[i]]<-ALL_dosages_a[which(phased.maplist[[i]][j,1] %in% rownames(ALL_dosages_a)),]
+	}
+
+
+}
+
+names(SNP_SSR)<-paste("LG",c(1:7),sep="")
+
+snpnameall<-phased.maplist
+
+for (i in 1: length(snpnameall)){
+	for (j in 1:length(snpnameall[[i]][,1])) {
+		if (length(which(snpnameall[[i]][j,1] %in% rownames(polymap_tetra[[1]])))) {
+			next
+	} else {
+	new<-polymap_tetra[[2]][which(snpnameall[[i]][j,1] %in% rownames(polymap_tetra[[1]])),]
+			rownames(SNP_SSR[[i]])[j]<-paste("c",new[,1],"_",new[,2],sep="")
+			#snpnameall[[i]][j,1]<-paste("c",new[,1],"_",new[,2],sep="")
+	}
+	}
+	snpnameall[[i]][,1]<-rownames(SNP_SSR[[i]])
+
+}
+
+
+
+for (i in 1: length(SNP_SSR)){
+	SNP_SSR[[i]][is.na(SNP_SSR[[i]])]<-9
+	write.table(SNP_SSR[[i]],file=paste("LGGEN",i,".txt",sep=""),quote=F,row.names=T,col.names=T)
+	}
+
+
+
+
+
+

R/OUPUT_MAP.R

@@ -0,0 +1,234 @@
+
+
+for(i in 1:7){
+  if(i==1){
+    integrated.maplist_P1[[i]] <- integrated.maplist_P1[[i]][-1046,]
+  } else if (i==4){
+    integrated.maplist_P1[[i]] <- integrated.maplist_P1[[i]][-659,]
+  }else{
+    integrated.maplist_P1[[i]] <- integrated.maplist_P1[[i]]
+  }
+
+  }
+
+
+
+for(i in 1:7){
+  if(i==2){
+    integrated.maplist_P2[[i]] <- integrated.maplist_P2[[i]][-1,]
+  } else if (i==4){
+    integrated.maplist_P2[[i]] <- integrated.maplist_P2[[i]][-1137,]
+  }else{
+    integrated.maplist_P2[[i]] <- integrated.maplist_P2[[i]]
+  }
+
+}
+
+
+
+for(i in 1:7){
+  if(i==1){
+    integrated.maplist[[i]] <- integrated.maplist[[i]][-1909,]
+  } else if (i==2){
+    integrated.maplist[[i]] <- integrated.maplist[[i]][-1,]
+  }else if (i==4){
+    integrated.maplist[[i]] <- integrated.maplist[[i]][-c(1,2,1399),]
+  }else {
+    integrated.maplist[[i]] <- integrated.maplist[[i]]
+  }
+
+  }
+
+
+
+alldt<-getwd()
+
+
+for(i in 1:7){
+  if (i==1){
+    #dir.create(paste("integrated.maplist_P1"))
+    #setwd(paste(alldt,"/integrated.maplist_P1",sep = ""))
+    write.csv(integrated.maplist_P1[[i]],
+                file=paste("integrated.maplist_P1_LG",i,".cvs",sep = ""),quote = F,row.names = F)
+    #dir.create(paste("integrated.maplist_P2"))
+    #setwd(paste(alldt,"/integrated.maplist_P2",sep = ""))
+    write.csv(integrated.maplist_P2[[i]],
+                file=paste("integrated.maplist_P2_LG",i,".csv",sep = ""),quote = F,row.names = F)
+    #dir.create(paste("integrated.maplist_all"))
+   # setwd(paste(alldt,"/integrated.maplist_all",sep = ""))
+    write.csv(integrated.maplist_P1[[i]],
+                file=paste("integrated.maplist_LG",i,".csv",sep = ""),quote = F,row.names = F)
+  }else {
+    #dir.create(paste("integrated.maplist_P1"))
+    #setwd(paste(alldt,"/integrated.maplist_P1",sep = ""))
+    write.csv(integrated.maplist_P1[[i]],
+                file=paste("integrated.maplist_P1_LG",i,".csv",sep = ""),quote = F,row.names = F)
+    #dir.create(paste("integrated.maplist_P2"))
+    #setwd(paste(alldt,"/integrated.maplist_P2",sep = ""))
+    write.csv(integrated.maplist_P2[[i]],
+                file=paste("integrated.maplist_P2_LG",i,".csv",sep = ""),quote = F,row.names = F)
+    #dir.create(paste("integrated.maplist_all"))
+    #setwd(paste(alldt,"/integrated.maplist_all",sep = ""))
+    write.csv(integrated.maplist_P1[[i]],
+                file=paste("integrated.maplist_LG",i,".csv",sep = ""),quote = F,row.names = F)
+
+  }
+
+}
+
+
+#dir.create(paste("integrated.maplist_P1"))
+#setwd(paste(getwd(),"/integrated.maplist_P1",sep = ""))
+all_P1<-do.call(rbind,integrated.maplist_P1)
+write.csv(all_P1,
+            file= "integrated.maplist_P1_all.csv",quote = F,row.names = F)
+
+#dir.create(paste("integrated.maplist_P2"))
+#setwd(paste(getwd(),"/integrated.maplist_P2",sep = ""))
+all_P2<-do.call(rbind,integrated.maplist_P2)
+write.csv(all_P1,
+            file= "integrated.maplist_P2_all.csv",quote = F,row.names = F)
+#dir.create(paste("integrated.maplist_all"))
+#setwd(paste(getwd(),"/integrated.maplist",sep = ""))
+all<-do.call(rbind,integrated.maplist_P2)
+write.csv(all,
+            file= "integrated.maplist_all.csv",quote = F,row.names = F)
+
+
+
+####output genetype
+map<-read.csv("polymap.map.tetra.csv",header=T)
+ALL_dos<-read.csv("polymap.20k.tetra.csv",header=T)
+
+ALL_dos<-read.csv("dosage_10x_snp.csv",header=T)
+map<-read.csv("dosage_10x_pos.csv",header=T)
+
+integrated.maplist_P1<-integrated.maplist_P1_chr1new
+
+###FATHER MAP
+MarN<-NULL;MapD<-NULL;AvD<-NULL;MaxG<-NULL;#Gap5cM<-NULL
+Position_P1<-list();Genetype_P1<-list()
+for(i in 1:7){
+  MarN[i]<-dim(integrated.maplist_P1[[i]])[1]
+  MapD[i]<-max(integrated.maplist_P1[[i]][,2])
+  AvD[i]<-max(integrated.maplist_P1[[i]][,2])/dim(integrated.maplist_P1[[i]])[1]
+  MaxG[i]<-max(integrated.maplist_P1[[i]][,2])-min(integrated.maplist_P1[[i]][,2])
+  #Gap5cM
+  Position_P1[[i]]<-map[which(ALL_dos$SNP %in% integrated.maplist_P1[[i]][,1]),]
+  Genetype_P1[[i]]<-ALL_dos[which(ALL_dos$SNP %in% integrated.maplist_P1[[i]][,1]),]
+  }
+
+phymap<-do.call(rbind,Position_P1)
+write.table(phymap,file="phymap_P1.txt",
+           quote = F,row.names = F,col.names = T)
+
+Genetype<-do.call(rbind,Genetype_P1)
+
+write.table(Genetype,file="Genetype_P1.txt",
+            quote = F,row.names = F,col.names = T)
+
+
+all_stats<-as.matrix(cbind(MarN,MapD,AvD,MaxG))
+
+colnames(all_stats)<-c("Mar Num","Map Distance","Aver Distance","Max Gap")
+
+for(i in 1:7){
+  rownames(all_stats)[i]<-paste("LG",i,sep = "")
+}
+write.csv(all_stats,file = "stats_P1.csv",quote=F,row.names=T)
+
+integrated.maplist_P2<-integrated.maplist_P2_chr1new
+
+####MOTHER MAP
+MarN<-NULL;MapD<-NULL;AvD<-NULL;MaxG<-NULL;#Gap5cM<-NULL
+Position_P2<-list();Genetype_P2<-list()
+for(i in 1:7){
+  MarN[i]<-dim(integrated.maplist_P2[[i]])[1]
+  MapD[i]<-max(integrated.maplist_P2[[i]][,2])
+  AvD[i]<-max(integrated.maplist_P2[[i]][,2])/dim(integrated.maplist_P2[[i]])[1]
+  MaxG[i]<-max(integrated.maplist_P2[[i]][,2])-min(integrated.maplist_P2[[i]][,2])
+  #Gap5cM
+  Position_P2[[i]]<-map[which(ALL_dos$SNP %in% integrated.maplist_P2[[i]][,1]),]
+  Genetype_P2[[i]]<-ALL_dos[which(ALL_dos$SNP %in% integrated.maplist_P2[[i]][,1]),]
+}
+
+phymap<-do.call(rbind,Position_P2)
+write.table(phymap,file="phymap_P2.txt",
+            quote = F,row.names = F,col.names = T)
+
+Genetype<-do.call(rbind,Genetype_P2)
+
+write.table(Genetype,file="Genetype_P2.txt",
+            quote = F,row.names = F,col.names = T)
+
+
+all_stats<-as.matrix(cbind(MarN,MapD,AvD,MaxG))
+
+colnames(all_stats)<-c("Mar Num","Map Distance","Aver Distance","Max Gap")
+
+for(i in 1:7){
+  rownames(all_stats)[i]<-paste("LG",i,sep = "")
+}
+write.csv(all_stats,file = "stats_P2.csv",quote=F,row.names=T)
+
+integrated.maplist<-integrated.maplist_chr1
+###INTEGRATE MAP
+MarN<-NULL;MapD<-NULL;AvD<-NULL;MaxG<-NULL;#Gap5cM<-NULL
+Position_PP<-list();Genetype_PP<-list()
+for(i in 1:7){
+  MarN[i]<-dim(integrated.maplist[[i]])[1]
+  MapD[i]<-max(integrated.maplist[[i]][,2])
+  AvD[i]<-max(integrated.maplist[[i]][,2])/dim(integrated.maplist[[i]])[1]
+  MaxG[i]<-max(integrated.maplist[[i]][,2])-min(integrated.maplist[[i]][,2])
+  #Gap5cM
+  Position_PP[[i]]<-map[which(ALL_dos$SNP %in% integrated.maplist[[i]][,1]),]
+  Genetype_PP[[i]]<-ALL_dos[which(ALL_dos$SNP %in% integrated.maplist[[i]][,1]),]
+}
+
+phymap<-do.call(rbind,Position_PP)
+write.table(phymap,file="phymap_PP.txt",
+            quote = F,row.names = F,col.names = T)
+
+Genetype<-do.call(rbind,Genetype_PP)
+
+write.table(Genetype,file="Genetype_PP.txt",
+            quote = F,row.names = F,col.names = T)
+
+
+all_stats<-as.matrix(cbind(MarN,MapD,AvD,MaxG))
+
+colnames(all_stats)<-c("Mar Num","Map Distance","Aver Distance","Max Gap")
+
+for(i in 1:7){
+  rownames(all_stats)[i]<-paste("LG",i,sep = "")
+}
+write.csv(all_stats,file = "stats_PP.csv",quote=F,row.names=T)
+
+
+
+
+
+
+
+
+
+
+
+
+
+chr<-unique(dis[,1])
+gap<-NULL
+
+for (i in 1:length(chr)){gap[i]<-max(dis[which(dis[,1] %in% chr[i]),2])-min(dis[which(dis[,1] %in% chr[i]),2])}
+
+
+
+
+
+
+
+
+
+
+
+