From b8bafad302138b13b3381aa768c2fe29142fa42c Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Tue, 20 Feb 2018 13:43:15 -0500
Subject: [PATCH] Updated by adding in output for average without zscore

---
 RAutoClDs.R | 90 +++++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 66 insertions(+), 24 deletions(-)

diff --git a/RAutoClDs.R b/RAutoClDs.R
index e26d4d7..6a7ea88 100644
--- a/RAutoClDs.R
+++ b/RAutoClDs.R
@@ -404,7 +404,26 @@ THEFT <- function(){
 				}
 				j <- j + 1
 			}
-			
+		
+		
+			##Outputting non Z-score Average over genes
+			newoutput <-NuRDATN
+			colnames(newoutput) <- rownames(tabRDATID)
+			nfnewout <- strsplit(alz,"[\\]") %>%
+	            .[[1]] %>%
+            	.[length(.)] %>%
+            	gsub("\\D","",.) %>%
+	            c("GSE",.,"newout.txt") %>%
+	            paste(collapse = "")
+            noutput <- newoutput %>%
+	            t()%>%
+	            as.data.frame(.,stringsAsFactors = FALSE)
+	    	noutput <- cbind(rownames(noutput),noutput)
+            colnames(noutput) <- c("Gene Symbol",subjnam)
+        	rownames(noutput) <- NULL
+            write.table(noutput, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE)
+            
+            
 			##Scaling the Data
 			scrawdat <- NuRDATN%>%
 				scale()
@@ -417,14 +436,17 @@ THEFT <- function(){
 	            .[[1]] %>%
             	.[length(.)] %>%
             	gsub("\\D","",.) %>%
-	            c("GSE",.,"zscore.txt") %>%
+	            c("GSE",.,"avg.txt") %>%
 	            paste(collapse = "")
             zscraw <- scrawdat %>%
 	            t()%>%
 	            as.data.frame(.,stringsAsFactors = FALSE)
-            colnames(zscraw) <- subjnam
-            write.table(zscraw, file = nfnzsc, sep = "\t",col.names = TRUE,row.names = TRUE)
-			
+	       	zscraw <- cbind(rownames(zscraw),zscraw)
+            colnames(zscraw) <- c("Gene Symbol",subjnam)
+        	rownames(zscraw) <- NULL
+            write.table(zscraw, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE)
+            
+            
 			##Discretized the Data
 			dialzdat <- scrawdat %>%
 				dndat(.) %>%
@@ -706,25 +728,45 @@ THEFT <- function(){
 					j <- j + 1
 				}
 				
-				##Scaling the Data
-				scrawdat <- NuRDATN%>%
-					scale()
-				attr(scrawdat,"scaled:center") <- NULL
-				attr(scrawdat,"scaled:scale") <- NULL
-				colnames(scrawdat) <- rownames(tabRDATID)
-				
-				#Outputting the Z-score file
-			    nfnzsc <- strsplit(alz,"[\\]") %>%
-                    .[[1]] %>%
-                    .[length(.)] %>%
-                    gsub("\\D","",.) %>%
-                    c("GSE",.,"zscore.txt") %>%
-                    paste(collapse = "")
-                zscraw <- scrawdat %>%
-                    t()%>%
-                    as.data.frame(.,stringsAsFactors = FALSE)
-                colnames(zscraw) <- subjnam
-                write.table(zscraw, file = nfnzsc, sep = "\t",col.names = TRUE,row.names = TRUE)
+				##Outputting non Z-score Average over genes
+			newoutput <-NuRDATN
+			colnames(newoutput) <- rownames(tabRDATID)
+			nfnewout <- strsplit(alz,"[\\]") %>%
+	            .[[1]] %>%
+            	.[length(.)] %>%
+            	gsub("\\D","",.) %>%
+	            c("GSE",.,"avg.txt") %>%
+	            paste(collapse = "")
+            noutput <- newoutput %>%
+	            t()%>%
+	            as.data.frame(.,stringsAsFactors = FALSE)
+	    	noutput <- cbind(rownames(noutput),noutput)
+            colnames(noutput) <- c("Gene Symbol",subjnam)
+        	rownames(noutput) <- NULL
+            write.table(noutput, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE)
+            
+            
+			##Scaling the Data
+			scrawdat <- NuRDATN%>%
+				scale()
+			attr(scrawdat,"scaled:center") <- NULL
+			attr(scrawdat,"scaled:scale") <- NULL
+			colnames(scrawdat) <- rownames(tabRDATID)
+			
+			#Outputting the Z-score file
+			nfnzsc <- strsplit(alz,"[\\]") %>%
+	            .[[1]] %>%
+            	.[length(.)] %>%
+            	gsub("\\D","",.) %>%
+	            c("GSE",.,"zscore.txt") %>%
+	            paste(collapse = "")
+            zscraw <- scrawdat %>%
+	            t()%>%
+	            as.data.frame(.,stringsAsFactors = FALSE)
+	       	zscraw <- cbind(rownames(zscraw),zscraw)
+            colnames(zscraw) <- c("Gene Symbol",subjnam)
+        	rownames(zscraw) <- NULL
+            write.table(zscraw, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE)
 				
 				##Discretized the Data
 				dialzdat <- scrawdat %>%
-- 
2.29.0