From da758df454781c9b5a48d30b9aaf7c8e4e994cf5 Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Tue, 20 Feb 2018 13:47:06 -0500
Subject: [PATCH] Updated outputting new file: average before z-score

---
 RCleanDscret.R | 61 +++++++++++++++++++++++++++++++++-----------------
 1 file changed, 41 insertions(+), 20 deletions(-)

diff --git a/RCleanDscret.R b/RCleanDscret.R
index f05f745..c311a3c 100644
--- a/RCleanDscret.R
+++ b/RCleanDscret.R
@@ -400,26 +400,47 @@ for(j in 1:length(tabRDATID)){
 	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 %>%
 	dndat(.) %>%
-- 
2.29.0