From 69ac507843530d76722471db7ddbf5f213a11aee Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Tue, 20 Jun 2017 15:03:46 -0400
Subject: [PATCH] Don't use this code yet Updated to decrease time of search
 for cgeneID

---
 RAutoClDs.R | 40 +++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/RAutoClDs.R b/RAutoClDs.R
index ac5e077..2e23841 100644
--- a/RAutoClDs.R
+++ b/RAutoClDs.R
@@ -104,20 +104,38 @@ NAFIXING <- function(GIDNAM){
 }	
 
 #4#Function for changing the gene ID to gene name
-cgeneID <- function(GeneName,DATA){
-    colGene <- dim(GeneName)[2]
-     j <- 1
-     for(j in 1:colGene){
-	chngsreq <- grep(paste0("^",GeneName[1,j],"$"),DATA[1,])
-	if(is.na(sum(chngsreq))==FALSE){
-		if(sum(chngsreq) > 0){
-			DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
+cgeneID2 <- function(GeneName,DATA){
+	nj <- t(GeneName)
+	nq <- t(DATA)
+	colGene <- dim(nj)[2]
+	colDATA <- dim(nq)[2]
+	j <- 1
+	for(j in 1:colDATA){
+		#where is that gene id located within the GPL file
+		chngreq <- grep(paste0("^",nq[1,j],"$"),nj[1,])
+		if(is.na(sum(chngreq))==FALSE){
+			if(sum(chngreq) > 0){
+			nq[1,j] <- gsub(paste0("^",nq[1,j],"$"),nj[2,chngreq],nq[1,j])
+			}
 		}
+		j <- j + 1
 	}
-	j = j+1
-	}
-	DATA
+	nq
 }
+#cgeneID <- function(GeneName,DATA){
+#    colGene <- dim(GeneName)[2]
+#     j <- 1
+#     for(j in 1:colGene){
+#	chngsreq <- grep(paste0("^",GeneName[1,j],"$"),DATA[1,])
+#	if(is.na(sum(chngsreq))==FALSE){
+#		if(sum(chngsreq) > 0){
+#			DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
+#		}
+#	}
+#	j = j+1
+#	}
+#	DATA
+#}
 
 #5#Function for adjusting the gene names
 gcnames <- function(DiData,usecol=1){
-- 
2.29.0