Added normWeightMode to computePred.R!

computePred.R

@@ -89,13 +89,57 @@ write.table(evolDist,paste0(prot,"_pred_evolEpi.txt"))
 print("done")
 
 print("running normalization...")
-#You should comment line 44 to use this functionality. Or maybe, it should go into normalize functions
-#That was what we originally decided with Alessandra. 
-#To get max values of PC, or Trace
-# trace = c()
-# print(trace)
-# for (row in 1:nrow(jet)) { trace<-append(trace, max(jet[row, "trace"], jet[row, "pc"])) }
-# print(trace)
+#normWeightMode="trace+pc+cv"
+#normWeightMode="trace+pc"
+#normWeightMode="trace+cv"
+normWeightMode="trace"
+#print(normWeightMode)
+#In future, you may need to comment line 44 to use this functionality if you do
+#weighting not just in normalization.
+#This part of the code obtains max values of Trace, PC, or CV for weighting the 
+#normalized results. 
+trace = c()
+if(normWeightMode=="trace+pc"){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) { 
+    if(sum(colnames(jet)=="traceMax")==1){
+      trace<-append(trace, max(jet[row, "traceMax"], jet[row, "pc"]))
+    }else{
+        trace<-append(trace, max(jet[row, "trace"], jet[row, "pc"]))
+    }
+  }
+} else if (normWeightMode=="trace+cv"){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) {
+    if(sum(colnames(jet)=="traceMax")==1){
+      trace<-append(trace, max(jet[row, "traceMax"], jet[row, "cv"]))
+    }else{
+        trace<-append(trace, max(jet[row, "trace"], jet[row, "cv"]))
+    } 
+  }
+} else if (normWeightMode=="trace+pc+cv"){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) {
+    if(sum(colnames(jet)=="traceMax")==1){
+      trace<-append(trace, max(jet[row, "traceMax"], max(jet[row, "pc"], jet[row, "cv"])))
+    }else{
+      trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "cv"])))
+    }
+  }
+} else if (normWeightMode=="trace"){
+  print("Using only JET2 traces")
+  for (row in 1:nrow(jet)) {
+    if(sum(colnames(jet)=="traceMax")==1){
+      trace<-append(trace, jet[row, "traceMax"])
+    }else{
+      trace<-append(trace, jet[row, "trace"])
+    } 
+  }
+}else{
+  print("ERROR: Unknown --normWeightMode selected!")
+  print("It can only be 'trace', 'trace+pc', 'trace+cv' or 'trace+pc+cv'!")
+}
+print(trace)
 
 if(simple){
   #Independent model normalization