From 39af88c5afa802b437df13de8a2b280baab041f2 Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Tue, 13 Jun 2017 15:16:39 -0400
Subject: [PATCH] fixed issue with spaces and choosing the second name
 (UNTESTED)

---
 RClean4.R | 36 +++++++++---------------------------
 1 file changed, 9 insertions(+), 27 deletions(-)

diff --git a/RClean4.R b/RClean4.R
index 8082f2e..781e99d 100644
--- a/RClean4.R
+++ b/RClean4.R
@@ -97,36 +97,18 @@ NAFIXING <- function(GIDNAM){
 	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(GeneName[1,j],DATA[1,])
-##		if(sum(chngsreq) > 0){
-##			#DATA[1,chngsreq] <- gsub(GeneName[1,j],GeneName[2,j],DATA[1,chngsreq])
-##			DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
-##		}
-##		j = j+1
-##	}
-##	DATA
-##}
 #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],"$"),DATA[1,])
-	if(is.na(sum(chngsreq))==FALSE){
-		if(sum(chngsreq) > 0){
-			DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
-		}
-	}
-		#if(sum(chngsreq) > 0){
-		##DATA[1,chngsreq] <- gsub(GeneName[1,j],GeneName[2,j],DATA[1,chngsreq])
-		#DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
-		#}
-	j = j+1
+	    chngsreq <- grep(paste0("^",GeneName[1,j],"$"),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
 }
@@ -138,9 +120,9 @@ gcnames <- function(DiData,usecol=1){
 	nwnam <- rep("0",length.out=nuruns)
 	for(i in 1:nuruns){
 		if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){
-			nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][usecol]
+			nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][usecol])
 		} else{
-			nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][1]
+			nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][1])
 		}
 		
 	}
-- 
2.29.0