From cb3deb0578045972ebb5540d8827f7516f0b3c4d Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Fri, 9 Jun 2017 14:34:26 -0400
Subject: [PATCH] Update that allows for more data set inputs at once

---
 RMatchGenes.R | 103 +++++++++++++++++++++++++++-----------------------
 1 file changed, 55 insertions(+), 48 deletions(-)

diff --git a/RMatchGenes.R b/RMatchGenes.R
index f93b92b..9777c12 100644
--- a/RMatchGenes.R
+++ b/RMatchGenes.R
@@ -6,57 +6,64 @@ library(readr)
 library(dplyr)
 
 Check2Match <- function(){
-#Bring in the two files
-##Number of rows with clinical data for first file
-numrow1 <- "How many rows of clinical data are their in the first data set?: " %>%
+    numrows <- "How many rows of clinical data are their in the each data set?: " %>%
 	readline(prompt = .) %>%
+	strsplit(.,split = ",") %>%
+	.[[1]] %>%
 	as.integer(.)
+    i <- 1
+    ANDIS <- select.list(choices = list.files(),multiple = TRUE, title = "Choose the file/files you want to analyze:")
 
-##Number of rows with clinical data for second file
-numrow2 <- "How many rows of clinical data are their in the second data set?: " %>%
-	readline(prompt = .) %>%
-	as.integer(.)
-
-edfile <- file.choose()
-ed <- edfile %>%
-	read_delim(.,delim = "\t")
-
-ednocd <- ed[-(1:numrow1),]
-eddfile <- file.choose()
-edd <- eddfile %>%
-	read_delim(.,delim = "\t")
+    for(i in 1:length(numrows)){
+	    if( i == 1){
+		    edfile <- ANDIS[i]
+		    ed <- edfile %>%
+			    read_delim(.,delim = "\t")
+		    ednocd <- ed[-(1:numrows[1]),]
+		    #Second file brought in
+		    eddfile <- ANDIS[i + 1]
+		    edd <- eddfile %>%
+			    read_delim(.,delim = "\t")	
+		    eddnocd <- edd[-(1:numrows[2]),]
+        
+		    ##Fully matched both data sets
+		    eddy <- inner_join(ednocd,eddnocd)
+		    #Matches		
+		    meds <- eddy[,1]
+		
+	    }	
+	    if(i > 1 && i + 1 < length(numrows)){
+		    eddfile <- ANDIS[i + 1]
+		    edd <- eddfile %>%
+		    	read_delim(.,delim = "\t")	
+		    eddnocd <- edd[-(1:numrows[i + 1]),]
+		    ##Fully matched both data sets
+		    eddy <- inner_join(meds,eddnocd)
+		    meds <- eddy[,1]
 	
-eddnocd <- edd[-(1:numrow2),]
-
-##Number of columns that belong to the first data file
-numbcol1 <- dim(ednocd)[2]
-##Number of columns that belong to the second data file
-numbcol2 <- dim(eddnocd)[2]
-
-##Fully matched both data sets
-eddy <- inner_join(ednocd,eddnocd)
-#Matched ed
-eddy[,1:numbcol1]
-Finedm <- rbind(ed[1:numrow1,],eddy[,1:numbcol1])
-nam_fil_ed <- strsplit(edfile,"[\\|/]") %>%
-			.[[1]] %>%
-			.[length(.)] %>%
-			gsub("\\D","",.) %>%
-			c("GSE",.,"matched.txt") %>%
-			paste(collapse = "")
-write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE)
-#Matched edd
-eddy[,(numbcol1 + 1):dim(eddy)[2]]
-fineddm <- cbind(eddy[,1],eddy[,(numbcol1 + 1):dim(eddy)[2]])
-Fineddm <- rbind(edd[1:numrow2,],fineddm)
-nam_fil_edd <- strsplit(eddfile,"[\\|/]") %>%
-			.[[1]] %>%
-			.[length(.)] %>%
-			gsub("\\D","",.) %>%
-			c("GSE",.,"matched.txt") %>%
-			paste(collapse = "")
-write.table(Fineddm,file = nam_fil_edd,sep = "\t",row.names = FALSE)
-
+		
+	    }
+	    i <- i + 1
+    }
+    meds
+    for(j in 1:length(numrows)){
+	    edfile <- ANDIS[j]
+	    ed <- edfile %>%
+    		read_delim(.,delim = "\t")
+    	ednocd <- ed[-(1:numrows[j]),]
+    	#use meds to match
+    	eddy <- inner_join(meds,ednocd)
+    	Finedm <- rbind(ed[1:numrows[j],],eddy)
+    	nam_fil_ed <- strsplit(edfile,"[\\|/]") %>%
+    		.[[1]] %>%
+    		.[length(.)] %>%
+    		gsub("\\D","",.) %>%
+    		c("GSE",.,"matched.txt") %>%
+    		paste(collapse = "")
+    	write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE)
+    	j <- j + 1
+    }
+    meds	
 }
 
-Check2Match()
+Check2Match()
\ No newline at end of file
-- 
2.29.0