New version which includes the storing of the clean version of the GPL file (UNTESTED)

Efrain Gonzalez
1 parent 18c7602e69
Showing 1 changed file with 302 additions and 0 deletions Show diff stats
RClean3.R
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+#Libraries required to run the code
+library(pryr)
+library(MASS)
+library(dplyr)
+library(tidyr)
+library(readr)
+library(stringr)
+
+
+#Necessary Functions
+#1#Function for handling the changing of row names and column names
+chngrownm <- function(mat){
+	row <- dim(mat)[1]
+	col <- dim(mat)[2]
+	j <- 1
+	x <- 1
+	p <- 1	
+	a <- 1
+	b <- 1
+	g <- 1
+	for(j in 1:col){
+		if("!Sample_source_name_ch1"==mat[1,j]){
+			colnames(mat)[j] <- "Brain_Region"	
+		} 
+		if("!Sample_title" == mat[1,j]){
+			colnames(mat)[j] <- "Title"
+		} 
+		if("!Sample_geo_accession" == mat[1,j]){
+			colnames(mat)[j] <- "ID_REF"
+		} else{
+			if(grepl("Sex|gender|Gender|sex",mat[2,j])==TRUE){
+				colnames(mat)[j] <- paste0("Sex",x)
+				x = x + 1
+			}
+			if(grepl("postmorteminterval|PMI|pmi",mat[2,j])==TRUE){
+				colnames(mat)[j] <- paste0("PMI",p)
+				p = p + 1
+			}
+			if(grepl("age|Age|AGE",mat[2,j])==TRUE){
+				colnames(mat)[j] <- paste0("Age",a)
+				a = a + 1
+			 }
+			if(grepl("braak|b&b",mat[2,j])==TRUE){
+				colnames(mat)[j] <- paste0("Braak",b)
+				b = b + 1
+			}
+			if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control",mat[2,j])==TRUE){
+				colnames(mat)[j] <- paste0("Group",g)
+				g = g + 1
+			}
+			
+		}
+		j = j + 1
+	}
+	mat
+}			
+
+#2#Function for reorganizing information within the columns
+cinfo <- function(mat){
+	col <- dim(mat)[2]
+	j <-2
+	for(j in 2:col){
+		if(grepl("Group",colnames(mat)[j]) == TRUE){
+			mat[,j] <- gsub(".+:\\s|\\s.+;.+","",mat[,j])
+		}
+		if(grepl("Age",colnames(mat)[j])==TRUE){
+			mat[,j] <- gsub("\\D","",mat[,j])%>%
+				as.integer()
+		}
+		if(grepl("Sex",colnames(mat)[j])==TRUE){
+			mat[,j] <- gsub(".+:\\s","",mat[,j])
+		}
+		if(grepl("PMI",colnames(mat)[j])==TRUE){
+			mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>%
+				as.numeric() 
+		}
+		if(grepl("Braak",colnames(mat)[j])==TRUE){
+			mat[,j]<-gsub(".+:\\s","",mat[,j])%>%
+				as.roman()%>%
+				as.integer()
+		}
+	j=j+1
+	}
+	mat
+}
+
+#3#Function for labeling the gene IDs without names
+NAFIXING <- function(GIDNAM){
+	row <- dim(GIDNAM)[1]
+	i <- 1
+	for(i in 1:row){
+		if(grepl("^NA\\s*$",GIDNAM[i,2])==TRUE||is.na(GIDNAM[i,2])==TRUE){
+			GIDNAM[i,2] <- GIDNAM[i,1]
+		}
+		i <- i + 1
+	}
+	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,])
+		#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
+}
+
+#5#Function for adjusting the gene names
+gcnames <- function(DiData,usecol=1){
+	nuruns <- dim(DiData)[2]
+	i = 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]
+		} else{
+			nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][1]
+		}
+		
+	}
+	nwnam
+
+}
+
+
+
+#The Rest of this code will be used every time you want to change a data set
+
+#Getting the series matrix file
+print("Choose the series matrix file that you want to Analyze")
+alz <- file.choose()
+
+#Getting the GPL file
+print("Choose the GPL file that correlates with the above series matrix file")
+genena <- file.choose()
+
+
+#Set working directory based on the directory of the series matrix file Currently only works for windows
+##strsplit(alz,"[\\]") %>%
+##	.[[1]] %>%
+##	.[-length(.)] %>%
+##	paste(.,collapse="/") %>%
+##	setwd()
+
+#Find out if it is a soft GPL file or not
+soft <- strsplit(genena,"[\\|/]") %>%
+	.[[1]] %>%
+	.[length(.)] %>%
+	grepl("soft",.)
+
+#Working with the wordy part of the document
+alzword <- alz %>%
+	read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>%
+	filter(grepl("!Sample",X1))%>%
+	filter(!grepl("!Sample_contact",X1))
+
+##Changing row names and column names:
+ALZWORD <- t(alzword)
+rownames(ALZWORD)=NULL
+colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE)
+ALZWORD <- chngrownm(ALZWORD)[-1,]
+ALZWORD <- ALZWORD%>%
+	as.data.frame()%>%
+	dplyr::select(-starts_with("col"))
+
+##Reorganizing information within the columns
+ALZWORDF <- cinfo(ALZWORD)
+
+
+#Working with Actual Data part of file
+alzdat <- alz %>% 
+	read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1)
+ALZDAT <- t(alzdat[,-1])
+rownames(ALZDAT)=NULL
+
+##Is there a clean version of the GPL file available?
+gplnum <- strsplit(genena,"[\\|/]") %>%
+	.[[1]] %>%
+	.[length(.)] %>%
+	gsub("\\D","",.)
+clfileex <- sum(grepl(paste0("Clean_GPL",gplnum),list.files()))
+if(clfileex >= 1){
+#use the clean version
+geneIDNam <-  paste0("Clean_GPL",gplnum,".txt") %>%
+	read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
+
+} 
+if(clfileex == 0){
+##Lets Create a clean version
+ 
+##Gene ID to Gene Name
+###geneIDNam <- genena %>%
+###	read_delim(delim="\t",comment = "#")%>%
+###	dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
+###problems with the above for soft files
+	if(soft == TRUE){
+		#gplnum <- strsplit(genena,"[\\|/]") %>%
+		#	.[[1]] %>%
+		#	.[length(.)] %>%
+		#	gsub("\\D","",.)
+		#Check to see if there is already a file containing information on soft files
+		fileex <- sum(grepl("GPL_ID_LOC.txt",list.files()))
+		if(fileex == 1){
+			#Check to see if this GPL soft file has been used before
+			IDF <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
+				.$GPL_FILE_NUM%>%
+				grepl(gplnum,.) %>%
+				sum()
+			if(IDF == 1){
+				IDLOCAL <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
+					.$GPL_FILE_NUM%>%
+					grep(gplnum,.)
+				idlocgpl <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
+					.$LOC_ID %>%
+					.[IDLOCAL]
+				geneIDNam <- genena %>%
+					read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
+					dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
+			}
+			if(IDF == 0){
+				#No information on this particular GPL file
+				idLOCGPL <- genena %>%
+					read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
+					t(.) %>%
+					grep("^\\D",.) %>%
+					length()-1
+				cbind(as.integer(gplnum),as.integer(idLOCGPL)) %>%
+					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",colnames(.)))
+			}
+		}
+		if(fileex == 0){
+			#We must create a file that we can access for later use
+			idLOCGPL <- genena %>%
+				read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
+				t(.) %>%
+				grep("^\\D",.) %>%
+				length()-1
+			Firstval <- cbind(as.integer(gplnum),as.integer(idLOCGPL))
+			colnames(Firstval) <- c("GPL_FILE_NUM","LOC_ID")
+			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",colnames(.)))
+		}
+	}
+	if(soft == FALSE){
+		geneIDNam <- genena %>%
+		read_delim(delim="\t",comment = "#")%>%
+		dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
+	}
+
+	##Labeling the gene IDs without names
+	geneIDNam <- NAFIXING(geneIDNam)	
+
+	##remove the whitespace
+	geneIDNam <- t(rbind(str_trim(t(geneIDNam)[1,]),str_trim(t(geneIDNam)[2,])))
+	
+	##Here is the clean version
+	write.table(geneIDNam,file = paste0("Clean_GPL",gplnum,".txt"),sep = "\t",row.names = FALSE, col.names = FALSE)
+}
+
+
+
+##Changing the gene ID to gene name
+ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat))
+colnames(ALZDAT) = ALZDAT1[1,]
+
+
+##Adjusting the column names aka the gene names
+colnames(ALZDAT) <- gcnames(ALZDAT)
+
+
+#Full Data
+Fullalzdw <- ALZDAT %>%
+	as.data.frame() %>%
+	cbind(ALZWORDF,.)
+
+
+#nfna <- strsplit(alz,"[\\|/]") %>%
+#	.[[1]] %>%
+#	.[length(.)] %>%
+#	gsub("\\D","",.) %>%
+#	c("GSE",.,"after.txt") %>%
+#	paste(collapse = "")
+#write.matrix(Fullalzdw,file = nfna,sep = "\t")
+
+#Perfect for excel viewing
+nfnaex <- strsplit(alz,"[\\]") %>%
+	.[[1]] %>%
+	.[length(.)] %>%
+	gsub("\\D","",.) %>%
+	c("GSE",.,"aftexcel.txt") %>%
+	paste(collapse = "")
+write.table(t(Fullalzdw), file = nfnaex, sep = "\t",row.names = FALSE)
 \ No newline at end of file
...	...	@@ -0,0 +1,302 @@
	1	+#Libraries required to run the code
	2	+library(pryr)
	3	+library(MASS)
	4	+library(dplyr)
	5	+library(tidyr)
	6	+library(readr)
	7	+library(stringr)
	8	+
	9	+
	10	+#Necessary Functions
	11	+#1#Function for handling the changing of row names and column names
	12	+chngrownm <- function(mat){
	13	+ row <- dim(mat)[1]
	14	+ col <- dim(mat)[2]
	15	+ j <- 1
	16	+ x <- 1
	17	+ p <- 1
	18	+ a <- 1
	19	+ b <- 1
	20	+ g <- 1
	21	+ for(j in 1:col){
	22	+ if("!Sample_source_name_ch1"==mat[1,j]){
	23	+ colnames(mat)[j] <- "Brain_Region"
	24	+ }
	25	+ if("!Sample_title" == mat[1,j]){
	26	+ colnames(mat)[j] <- "Title"
	27	+ }
	28	+ if("!Sample_geo_accession" == mat[1,j]){
	29	+ colnames(mat)[j] <- "ID_REF"
	30	+ } else{
	31	+ if(grepl("Sex\|gender\|Gender\|sex",mat[2,j])==TRUE){
	32	+ colnames(mat)[j] <- paste0("Sex",x)
	33	+ x = x + 1
	34	+ }
	35	+ if(grepl("postmorteminterval\|PMI\|pmi",mat[2,j])==TRUE){
	36	+ colnames(mat)[j] <- paste0("PMI",p)
	37	+ p = p + 1
	38	+ }
	39	+ if(grepl("age\|Age\|AGE",mat[2,j])==TRUE){
	40	+ colnames(mat)[j] <- paste0("Age",a)
	41	+ a = a + 1
	42	+ }
	43	+ if(grepl("braak\|b&b",mat[2,j])==TRUE){
	44	+ colnames(mat)[j] <- paste0("Braak",b)
	45	+ b = b + 1
	46	+ }
	47	+ if(grepl("group\|disease\|control\|AD\|normal\|diagnosis\|Alzheimer\|Control",mat[2,j])==TRUE){
	48	+ colnames(mat)[j] <- paste0("Group",g)
	49	+ g = g + 1
	50	+ }
	51	+
	52	+ }
	53	+ j = j + 1
	54	+ }
	55	+ mat
	56	+}
	57	+
	58	+#2#Function for reorganizing information within the columns
	59	+cinfo <- function(mat){
	60	+ col <- dim(mat)[2]
	61	+ j <-2
	62	+ for(j in 2:col){
	63	+ if(grepl("Group",colnames(mat)[j]) == TRUE){
	64	+ mat[,j] <- gsub(".+:\\s\|\\s.+;.+","",mat[,j])
	65	+ }
	66	+ if(grepl("Age",colnames(mat)[j])==TRUE){
	67	+ mat[,j] <- gsub("\\D","",mat[,j])%>%
	68	+ as.integer()
	69	+ }
	70	+ if(grepl("Sex",colnames(mat)[j])==TRUE){
	71	+ mat[,j] <- gsub(".+:\\s","",mat[,j])
	72	+ }
	73	+ if(grepl("PMI",colnames(mat)[j])==TRUE){
	74	+ mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>%
	75	+ as.numeric()
	76	+ }
	77	+ if(grepl("Braak",colnames(mat)[j])==TRUE){
	78	+ mat[,j]<-gsub(".+:\\s","",mat[,j])%>%
	79	+ as.roman()%>%
	80	+ as.integer()
	81	+ }
	82	+ j=j+1
	83	+ }
	84	+ mat
	85	+}
	86	+
	87	+#3#Function for labeling the gene IDs without names
	88	+NAFIXING <- function(GIDNAM){
	89	+ row <- dim(GIDNAM)[1]
	90	+ i <- 1
	91	+ for(i in 1:row){
	92	+ if(grepl("^NA\\s*$",GIDNAM[i,2])==TRUE\|\|is.na(GIDNAM[i,2])==TRUE){
	93	+ GIDNAM[i,2] <- GIDNAM[i,1]
	94	+ }
	95	+ i <- i + 1
	96	+ }
	97	+ GIDNAM
	98	+}
	99	+
	100	+#4#Function for changing the gene ID to gene name
	101	+cgeneID <- function(GeneName,DATA){
	102	+ colGene <- dim(GeneName)[2]
	103	+ j <- 1
	104	+ for(j in 1:colGene){
	105	+ chngsreq <- grep(GeneName[1,j],DATA[1,])
	106	+ #DATA[1,chngsreq] <- gsub(GeneName[1,j],GeneName[2,j],DATA[1,chngsreq])
	107	+ DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
	108	+ j = j+1
	109	+ }
	110	+ DATA
	111	+}
	112	+
	113	+#5#Function for adjusting the gene names
	114	+gcnames <- function(DiData,usecol=1){
	115	+ nuruns <- dim(DiData)[2]
	116	+ i = 1
	117	+ nwnam <- rep("0",length.out=nuruns)
	118	+ for(i in 1:nuruns){
	119	+ if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){
	120	+ nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][usecol]
	121	+ } else{
	122	+ nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][1]
	123	+ }
	124	+
	125	+ }
	126	+ nwnam
	127	+
	128	+}
	129	+
	130	+
	131	+
	132	+#The Rest of this code will be used every time you want to change a data set
	133	+
	134	+#Getting the series matrix file
	135	+print("Choose the series matrix file that you want to Analyze")
	136	+alz <- file.choose()
	137	+
	138	+#Getting the GPL file
	139	+print("Choose the GPL file that correlates with the above series matrix file")
	140	+genena <- file.choose()
	141	+
	142	+
	143	+#Set working directory based on the directory of the series matrix file Currently only works for windows
	144	+##strsplit(alz,"[\\]") %>%
	145	+## .[[1]] %>%
	146	+## .[-length(.)] %>%
	147	+## paste(.,collapse="/") %>%
	148	+## setwd()
	149	+
	150	+#Find out if it is a soft GPL file or not
	151	+soft <- strsplit(genena,"[\\\|/]") %>%
	152	+ .[[1]] %>%
	153	+ .[length(.)] %>%
	154	+ grepl("soft",.)
	155	+
	156	+#Working with the wordy part of the document
	157	+alzword <- alz %>%
	158	+ read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>%
	159	+ filter(grepl("!Sample",X1))%>%
	160	+ filter(!grepl("!Sample_contact",X1))
	161	+
	162	+##Changing row names and column names:
	163	+ALZWORD <- t(alzword)
	164	+rownames(ALZWORD)=NULL
	165	+colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE)
	166	+ALZWORD <- chngrownm(ALZWORD)[-1,]
	167	+ALZWORD <- ALZWORD%>%
	168	+ as.data.frame()%>%
	169	+ dplyr::select(-starts_with("col"))
	170	+
	171	+##Reorganizing information within the columns
	172	+ALZWORDF <- cinfo(ALZWORD)
	173	+
	174	+
	175	+#Working with Actual Data part of file
	176	+alzdat <- alz %>%
	177	+ read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1)
	178	+ALZDAT <- t(alzdat[,-1])
	179	+rownames(ALZDAT)=NULL
	180	+
	181	+##Is there a clean version of the GPL file available?
	182	+gplnum <- strsplit(genena,"[\\\|/]") %>%
	183	+ .[[1]] %>%
	184	+ .[length(.)] %>%
	185	+ gsub("\\D","",.)
	186	+clfileex <- sum(grepl(paste0("Clean_GPL",gplnum),list.files()))
	187	+if(clfileex >= 1){
	188	+#use the clean version
	189	+geneIDNam <- paste0("Clean_GPL",gplnum,".txt") %>%
	190	+ read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
	191	+
	192	+}
	193	+if(clfileex == 0){
	194	+##Lets Create a clean version
	195	+
	196	+##Gene ID to Gene Name
	197	+###geneIDNam <- genena %>%
	198	+### read_delim(delim="\t",comment = "#")%>%
	199	+### dplyr::select(.,ID,grep("Symbol\|ORF",colnames(.)))
	200	+###problems with the above for soft files
	201	+ if(soft == TRUE){
	202	+ #gplnum <- strsplit(genena,"[\\\|/]") %>%
	203	+ # .[[1]] %>%
	204	+ # .[length(.)] %>%
	205	+ # gsub("\\D","",.)
	206	+ #Check to see if there is already a file containing information on soft files
	207	+ fileex <- sum(grepl("GPL_ID_LOC.txt",list.files()))
	208	+ if(fileex == 1){
	209	+ #Check to see if this GPL soft file has been used before
	210	+ IDF <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
	211	+ .$GPL_FILE_NUM%>%
	212	+ grepl(gplnum,.) %>%
	213	+ sum()
	214	+ if(IDF == 1){
	215	+ IDLOCAL <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
	216	+ .$GPL_FILE_NUM%>%
	217	+ grep(gplnum,.)
	218	+ idlocgpl <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
	219	+ .$LOC_ID %>%
	220	+ .[IDLOCAL]
	221	+ geneIDNam <- genena %>%
	222	+ read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
	223	+ dplyr::select(.,ID,grep("Symbol\|ORF",colnames(.)))
	224	+ }
	225	+ if(IDF == 0){
	226	+ #No information on this particular GPL file
	227	+ idLOCGPL <- genena %>%
	228	+ read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
	229	+ t(.) %>%
	230	+ grep("^\\D",.) %>%
	231	+ length()-1
	232	+ cbind(as.integer(gplnum),as.integer(idLOCGPL)) %>%
	233	+ cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE)
	234	+ geneIDNam <- genena %>%
	235	+ read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
	236	+ dplyr::select(.,ID,grep("Symbol\|ORF",colnames(.)))
	237	+ }
	238	+ }
	239	+ if(fileex == 0){
	240	+ #We must create a file that we can access for later use
	241	+ idLOCGPL <- genena %>%
	242	+ read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
	243	+ t(.) %>%
	244	+ grep("^\\D",.) %>%
	245	+ length()-1
	246	+ Firstval <- cbind(as.integer(gplnum),as.integer(idLOCGPL))
	247	+ colnames(Firstval) <- c("GPL_FILE_NUM","LOC_ID")
	248	+ write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE)
	249	+ geneIDNam <- genena %>%
	250	+ read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
	251	+ dplyr::select(.,ID,grep("Symbol\|ORF",colnames(.)))
	252	+ }
	253	+ }
	254	+ if(soft == FALSE){
	255	+ geneIDNam <- genena %>%
	256	+ read_delim(delim="\t",comment = "#")%>%
	257	+ dplyr::select(.,ID,grep("Symbol\|ORF",colnames(.)))
	258	+ }
	259	+
	260	+ ##Labeling the gene IDs without names
	261	+ geneIDNam <- NAFIXING(geneIDNam)
	262	+
	263	+ ##remove the whitespace
	264	+ geneIDNam <- t(rbind(str_trim(t(geneIDNam)[1,]),str_trim(t(geneIDNam)[2,])))
	265	+
	266	+ ##Here is the clean version
	267	+ write.table(geneIDNam,file = paste0("Clean_GPL",gplnum,".txt"),sep = "\t",row.names = FALSE, col.names = FALSE)
	268	+}
	269	+
	270	+
	271	+
	272	+##Changing the gene ID to gene name
	273	+ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat))
	274	+colnames(ALZDAT) = ALZDAT1[1,]
	275	+
	276	+
	277	+##Adjusting the column names aka the gene names
	278	+colnames(ALZDAT) <- gcnames(ALZDAT)
	279	+
	280	+
	281	+#Full Data
	282	+Fullalzdw <- ALZDAT %>%
	283	+ as.data.frame() %>%
	284	+ cbind(ALZWORDF,.)
	285	+
	286	+
	287	+#nfna <- strsplit(alz,"[\\\|/]") %>%
	288	+# .[[1]] %>%
	289	+# .[length(.)] %>%
	290	+# gsub("\\D","",.) %>%
	291	+# c("GSE",.,"after.txt") %>%
	292	+# paste(collapse = "")
	293	+#write.matrix(Fullalzdw,file = nfna,sep = "\t")
	294	+
	295	+#Perfect for excel viewing
	296	+nfnaex <- strsplit(alz,"[\\]") %>%
	297	+ .[[1]] %>%
	298	+ .[length(.)] %>%
	299	+ gsub("\\D","",.) %>%
	300	+ c("GSE",.,"aftexcel.txt") %>%
	301	+ paste(collapse = "")
	302	+write.table(t(Fullalzdw), file = nfnaex, sep = "\t",row.names = FALSE)
0	303	\ No newline at end of file