From 48208ef1ad8e4050e3d595fb12b0e20a87d174e4 Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Thu, 5 Apr 2018 15:08:46 -0400
Subject: [PATCH] Update added |^UCSC_RefGene_Name$ to list of potential names
 in GPL

---
 RAutoClDs.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/RAutoClDs.R b/RAutoClDs.R
index 815b534..7e648ad 100644
--- a/RAutoClDs.R
+++ b/RAutoClDs.R
@@ -264,7 +264,7 @@ THEFT <- function(){
 									.[IDLOCAL]
 							geneIDNam <- genena %>%
 								read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
-								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 						} else if(IDF == 0){
 							#No information on this particular GPL file
 							idLOCGPL <- genena %>%
@@ -276,7 +276,7 @@ THEFT <- function(){
 								cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE)
 							geneIDNam <- genena %>%
 								read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
-								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 						}
 					} else if(fileex == 0){
 						#We must create a file that we can access for later use
@@ -290,12 +290,12 @@ THEFT <- function(){
 						write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE)
 						geneIDNam <- genena %>%
 							read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
-							dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+							dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 					}
 	 			} else if(soft == FALSE){
 					geneIDNam <- genena %>%
 						read_delim(delim="\t",comment = "#")%>%
-						dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+						dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 				}
 				
 				##Labeling the gene IDs without names
@@ -587,7 +587,7 @@ THEFT <- function(){
 										.[IDLOCAL]
 								geneIDNam <- genena %>%
 									read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
-									dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+									dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 							} else if(IDF == 0){
 								#No information on this particular GPL file
 								idLOCGPL <- genena %>%
@@ -599,7 +599,7 @@ THEFT <- function(){
 									cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE)
 								geneIDNam <- genena %>%
 									read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
-									dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+									dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 							}
 						} else if(fileex == 0){
 							#We must create a file that we can access for later use
@@ -613,12 +613,12 @@ THEFT <- function(){
 							write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE)
 							geneIDNam <- genena %>%
 								read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
-								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+								dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 						}
 		 			} else if(soft == FALSE){
 						geneIDNam <- genena %>%
 							read_delim(delim="\t",comment = "#")%>%
-							dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.)))
+							dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$|^UCSC_RefGene_Name$",colnames(.)))
 					}
 					
 					##Labeling the gene IDs without names
-- 
2.29.0