Efrain Gonzalez / Cleaning and Fixing Data with R

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Commit 01a09e19c46fc5cb60074c9f5bb59da18fb77c54

Authored by Efrain Gonzalez
1 parent 83db0077e4
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moved old file to this folder

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1 #Libraries required to run the code 1 #Libraries required to run the code
2 library(pryr) 2 library(pryr)
3 library(MASS) 3 library(MASS)
4 library(dplyr) 4 library(dplyr)
5 library(tidyr) 5 library(tidyr)
6 library(readr) 6 library(readr)
7 library(stringr) 7 library(stringr)
8 8
9 9
10 #Necessary Functions 10 #Necessary Functions
11 #1#Function for handling the changing of row names and column names 11 #1#Function for handling the changing of row names and column names
12 chngrownm <- function(mat){ 12 chngrownm <- function(mat){
13 row <- dim(mat)[1] 13 row <- dim(mat)[1]
14 col <- dim(mat)[2] 14 col <- dim(mat)[2]
15 j <- 1 15 j <- 1
16 x <- 1 16 x <- 1
17 p <- 1 17 p <- 1
18 a <- 1 18 a <- 1
19 b <- 1 19 b <- 1
20 g <- 1 20 g <- 1
21 for(j in 1:col){ 21 for(j in 1:col){
22 if("!Sample_source_name_ch1"==mat[1,j]){ 22 if("!Sample_source_name_ch1"==mat[1,j]){
23 colnames(mat)[j] <- "Brain_Region" 23 colnames(mat)[j] <- "Brain_Region"
24 } 24 }
25 if("!Sample_title" == mat[1,j]){ 25 if("!Sample_title" == mat[1,j]){
26 colnames(mat)[j] <- "Title" 26 colnames(mat)[j] <- "Title"
27 } 27 }
28 if("!Sample_geo_accession" == mat[1,j]){ 28 if("!Sample_geo_accession" == mat[1,j]){
29 colnames(mat)[j] <- "ID_REF" 29 colnames(mat)[j] <- "ID_REF"
30 } else{ 30 } else{
31 if(grepl("Sex|gender|Gender|sex",mat[2,j])==TRUE){ 31 if(grepl("Sex|gender|Gender|sex",mat[2,j])==TRUE){
32 colnames(mat)[j] <- paste0("Sex",x) 32 colnames(mat)[j] <- paste0("Sex",x)
33 x = x + 1 33 x = x + 1
34 } 34 }
35 if(grepl("postmorteminterval|PMI|pmi",mat[2,j])==TRUE){ 35 if(grepl("postmorteminterval|PMI|pmi",mat[2,j])==TRUE){
36 colnames(mat)[j] <- paste0("PMI",p) 36 colnames(mat)[j] <- paste0("PMI",p)
37 p = p + 1 37 p = p + 1
38 } 38 }
39 if(grepl("age|Age|AGE",mat[2,j])==TRUE){ 39 if(grepl("age|Age|AGE",mat[2,j])==TRUE){
40 colnames(mat)[j] <- paste0("Age",a) 40 colnames(mat)[j] <- paste0("Age",a)
41 a = a + 1 41 a = a + 1
42 } 42 }
43 if(grepl("braak|b&b",mat[2,j])==TRUE){ 43 if(grepl("braak|b&b",mat[2,j])==TRUE){
44 colnames(mat)[j] <- paste0("Braak",b) 44 colnames(mat)[j] <- paste0("Braak",b)
45 b = b + 1 45 b = b + 1
46 } 46 }
47 if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control|Normal",mat[2,j])==TRUE){ 47 if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control|Normal",mat[2,j])==TRUE){
48 colnames(mat)[j] <- paste0("Group",g) 48 colnames(mat)[j] <- paste0("Group",g)
49 g = g + 1 49 g = g + 1
50 } 50 }
51 51
52 } 52 }
53 j = j + 1 53 j = j + 1
54 } 54 }
55 mat 55 mat
56 } 56 }
57 57
58 #2#Function for reorganizing information within the columns 58 #2#Function for reorganizing information within the columns
59 cinfo <- function(mat){ 59 cinfo <- function(mat){
60 col <- dim(mat)[2] 60 col <- dim(mat)[2]
61 j <-2 61 j <-2
62 for(j in 2:col){ 62 for(j in 2:col){
63 if(grepl("Group",colnames(mat)[j]) == TRUE){ 63 if(grepl("Group",colnames(mat)[j]) == TRUE){
64 mat[,j] <- gsub(".+:\\s|\\s.+;.+","",mat[,j]) 64 mat[,j] <- gsub(".+:\\s|\\s.+;.+","",mat[,j])
65 } 65 }
66 if(grepl("Age",colnames(mat)[j])==TRUE){ 66 if(grepl("Age",colnames(mat)[j])==TRUE){
67 mat[,j] <- gsub("\\D","",mat[,j])%>% 67 mat[,j] <- gsub("\\D","",mat[,j])%>%
68 as.integer() 68 as.integer()
69 } 69 }
70 if(grepl("Sex",colnames(mat)[j])==TRUE){ 70 if(grepl("Sex",colnames(mat)[j])==TRUE){
71 mat[,j] <- gsub(".+:\\s","",mat[,j]) 71 mat[,j] <- gsub(".+:\\s","",mat[,j])
72 } 72 }
73 if(grepl("PMI",colnames(mat)[j])==TRUE){ 73 if(grepl("PMI",colnames(mat)[j])==TRUE){
74 mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>% 74 mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>%
75 as.numeric() 75 as.numeric()
76 } 76 }
77 if(grepl("Braak",colnames(mat)[j])==TRUE){ 77 if(grepl("Braak",colnames(mat)[j])==TRUE){
78 mat[,j]<-gsub(".+:\\s","",mat[,j])%>% 78 mat[,j]<-gsub(".+:\\s","",mat[,j])%>%
79 as.roman()%>% 79 as.roman()%>%
80 as.integer() 80 as.integer()
81 } 81 }
82 j=j+1 82 j=j+1
83 } 83 }
84 mat 84 mat
85 } 85 }
86 86
87 #3#Function for labeling the gene IDs without names 87 #3#Function for labeling the gene IDs without names
88 NAFIXING <- function(GIDNAM){ 88 NAFIXING <- function(GIDNAM){
89 row <- dim(GIDNAM)[1] 89 row <- dim(GIDNAM)[1]
90 i <- 1 90 i <- 1
91 for(i in 1:row){ 91 for(i in 1:row){
92 if(grepl("^NA\\s*$",GIDNAM[i,2])==TRUE||is.na(GIDNAM[i,2])==TRUE){ 92 if(grepl("^NA\\s*$",GIDNAM[i,2])==TRUE||is.na(GIDNAM[i,2])==TRUE){
93 GIDNAM[i,2] <- GIDNAM[i,1] 93 GIDNAM[i,2] <- GIDNAM[i,1]
94 } 94 }
95 i <- i + 1 95 i <- i + 1
96 } 96 }
97 GIDNAM 97 GIDNAM
98 } 98 }
99 99
100 #4#Function for changing the gene ID to gene name 100 #4#Function for changing the gene ID to gene name
101 cgeneID <- function(GeneName,DATA){ 101 cgeneID <- function(GeneName,DATA){
102 colGene <- dim(GeneName)[2] 102 colGene <- dim(GeneName)[2]
103 j <- 1 103 j <- 1
104 for(j in 1:colGene){ 104 for(j in 1:colGene){
105 chngsreq <- grep(paste0("^",GeneName[1,j],"$"),DATA[1,]) 105 chngsreq <- grep(paste0("^",GeneName[1,j],"$"),DATA[1,])
106 if(is.na(sum(chngsreq))==FALSE){ 106 if(is.na(sum(chngsreq))==FALSE){
107 if(sum(chngsreq) > 0){ 107 if(sum(chngsreq) > 0){
108 DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq]) 108 DATA[1,chngsreq] <- gsub(paste0("^",GeneName[1,j]),GeneName[2,j],DATA[1,chngsreq])
109 } 109 }
110 } 110 }
111 j = j+1 111 j = j+1
112 } 112 }
113 DATA 113 DATA
114 } 114 }
115 115
116 #5#Function for adjusting the gene names 116 #5#Function for adjusting the gene names
117 gcnames <- function(DiData,usecol=1){ 117 gcnames <- function(DiData,usecol=1){
118 nuruns <- dim(DiData)[2] 118 nuruns <- dim(DiData)[2]
119 i = 1 119 i = 1
120 nwnam <- rep("0",length.out=nuruns) 120 nwnam <- rep("0",length.out=nuruns)
121 for(i in 1:nuruns){ 121 for(i in 1:nuruns){
122 if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){ 122 if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){
123 nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][usecol]) 123 nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][usecol])
124 } else{ 124 } else{
125 nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][1]) 125 nwnam[i]=str_trim(strsplit(colnames(DiData)[i],"///")[[1]][1])
126 } 126 }
127 127
128 } 128 }
129 nwnam 129 nwnam
130 130
131 } 131 }
132 132
133 133
134 134
135 #The Rest of this code will be used every time you want to change a data set 135 #The Rest of this code will be used every time you want to change a data set
136 136
137 #Getting the series matrix file 137 #Getting the series matrix file
138 print("Choose the series matrix file that you want to Analyze") 138 print("Choose the series matrix file that you want to Analyze")
139 alz <- file.choose() 139 alz <- file.choose()
140 140
141 #Getting the GPL file 141 #Getting the GPL file
142 print("Choose the GPL file that correlates with the above series matrix file") 142 print("Choose the GPL file that correlates with the above series matrix file")
143 genena <- file.choose() 143 genena <- file.choose()
144 144
145 145
146 #Set working directory based on the directory of the series matrix file Currently only works for windows 146 #Set working directory based on the directory of the series matrix file Currently only works for windows
147 ##strsplit(alz,"[\\]") %>% 147 ##strsplit(alz,"[\\]") %>%
148 ## .[[1]] %>% 148 ## .[[1]] %>%
149 ## .[-length(.)] %>% 149 ## .[-length(.)] %>%
150 ## paste(.,collapse="/") %>% 150 ## paste(.,collapse="/") %>%
151 ## setwd() 151 ## setwd()
152 152
153 #Find out if it is a soft GPL file or not 153 #Find out if it is a soft GPL file or not
154 soft <- strsplit(genena,"[\\|/]") %>% 154 soft <- strsplit(genena,"[\\|/]") %>%
155 .[[1]] %>% 155 .[[1]] %>%
156 .[length(.)] %>% 156 .[length(.)] %>%
157 grepl("soft|annot",.) 157 grepl("soft|annot",.)
158 158
159 #Working with the wordy part of the document 159 #Working with the wordy part of the document
160 alzword <- alz %>% 160 alzword <- alz %>%
161 read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>% 161 read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>%
162 filter(grepl("!Sample",X1))%>% 162 filter(grepl("!Sample",X1))%>%
163 filter(!grepl("!Sample_contact",X1)) 163 filter(!grepl("!Sample_contact",X1))
164 164
165 ##Changing row names and column names: 165 ##Changing row names and column names:
166 ALZWORD <- t(alzword) 166 ALZWORD <- t(alzword)
167 rownames(ALZWORD)=NULL 167 rownames(ALZWORD)=NULL
168 colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE) 168 colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE)
169 ALZWORD <- chngrownm(ALZWORD)[-1,] 169 ALZWORD <- chngrownm(ALZWORD)[-1,]
170 ALZWORD <- ALZWORD%>% 170 ALZWORD <- ALZWORD%>%
171 as.data.frame()%>% 171 as.data.frame()%>%
172 dplyr::select(-starts_with("col")) 172 dplyr::select(-starts_with("col"))
173 173
174 ##Reorganizing information within the columns 174 ##Reorganizing information within the columns
175 ALZWORDF <- cinfo(ALZWORD) 175 ALZWORDF <- cinfo(ALZWORD)
176 176
177 177
178 #Working with Actual Data part of file 178 #Working with Actual Data part of file
179 alzdat <- alz %>% 179 alzdat <- alz %>%
180 read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1) 180 read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1)
181 ALZDAT <- t(alzdat[,-1]) 181 ALZDAT <- t(alzdat[,-1])
182 rownames(ALZDAT)=NULL 182 rownames(ALZDAT)=NULL
183 183
184 ##Is there a clean version of the GPL file available? 184 ##Is there a clean version of the GPL file available?
185 gplnum <- strsplit(genena,"[\\|/]") %>% 185 gplnum <- strsplit(genena,"[\\|/]") %>%
186 .[[1]] %>% 186 .[[1]] %>%
187 .[length(.)] %>% 187 .[length(.)] %>%
188 gsub("\\D","",.) 188 gsub("\\D","",.)
189 clfileex <- sum(grepl(paste0("Clean_GPL",gplnum),list.files())) 189 clfileex <- sum(grepl(paste0("Clean_GPL",gplnum),list.files()))
190 if(clfileex >= 1){ 190 if(clfileex >= 1){
191 #use the clean version 191 #use the clean version
192 geneIDNam <- paste0("Clean_GPL",gplnum,".txt") %>% 192 geneIDNam <- paste0("Clean_GPL",gplnum,".txt") %>%
193 read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!") 193 read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
194 194
195 } 195 }
196 if(clfileex == 0){ 196 if(clfileex == 0){
197 ##Lets Create a clean version 197 ##Lets Create a clean version
198 198
199 ##Gene ID to Gene Name 199 ##Gene ID to Gene Name
200 ###geneIDNam <- genena %>% 200 ###geneIDNam <- genena %>%
201 ### read_delim(delim="\t",comment = "#")%>% 201 ### read_delim(delim="\t",comment = "#")%>%
202 ### dplyr::select(.,ID,grep("Symbol|ORF",colnames(.))) 202 ### dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
203 ###problems with the above for soft files 203 ###problems with the above for soft files
204 if(soft == TRUE){ 204 if(soft == TRUE){
205 #gplnum <- strsplit(genena,"[\\|/]") %>% 205 #gplnum <- strsplit(genena,"[\\|/]") %>%
206 # .[[1]] %>% 206 # .[[1]] %>%
207 # .[length(.)] %>% 207 # .[length(.)] %>%
208 # gsub("\\D","",.) 208 # gsub("\\D","",.)
209 #Check to see if there is already a file containing information on soft files 209 #Check to see if there is already a file containing information on soft files
210 fileex <- sum(grepl("GPL_ID_LOC.txt",list.files())) 210 fileex <- sum(grepl("GPL_ID_LOC.txt",list.files()))
211 if(fileex == 1){ 211 if(fileex == 1){
212 #Check to see if this GPL soft file has been used before 212 #Check to see if this GPL soft file has been used before
213 IDF <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>% 213 IDF <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
214 .$GPL_FILE_NUM%>% 214 .$GPL_FILE_NUM%>%
215 grepl(gplnum,.) %>% 215 grepl(gplnum,.) %>%
216 sum() 216 sum()
217 if(IDF == 1){ 217 if(IDF == 1){
218 IDLOCAL <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>% 218 IDLOCAL <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
219 .$GPL_FILE_NUM%>% 219 .$GPL_FILE_NUM%>%
220 grep(gplnum,.) 220 grep(gplnum,.)
221 idlocgpl <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>% 221 idlocgpl <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
222 .$LOC_ID %>% 222 .$LOC_ID %>%
223 .[IDLOCAL] 223 .[IDLOCAL]
224 geneIDNam <- genena %>% 224 geneIDNam <- genena %>%
225 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>% 225 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
226 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.))) 226 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
227 } 227 }
228 if(IDF == 0){ 228 if(IDF == 0){
229 #No information on this particular GPL file 229 #No information on this particular GPL file
230 idLOCGPL <- genena %>% 230 idLOCGPL <- genena %>%
231 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>% 231 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
232 t(.) %>% 232 t(.) %>%
233 .[1,] %>% 233 .[1,] %>%
234 grep("^ID\\s*$",.) %>% 234 grep("^ID\\s*$",.) %>%
235 -1 235 -1
236 cbind(as.integer(gplnum),as.integer(idLOCGPL)) %>% 236 cbind(as.integer(gplnum),as.integer(idLOCGPL)) %>%
237 cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE) 237 cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE)
238 geneIDNam <- genena %>% 238 geneIDNam <- genena %>%
239 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% 239 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
240 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.))) 240 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
241 } 241 }
242 } 242 }
243 if(fileex == 0){ 243 if(fileex == 0){
244 #We must create a file that we can access for later use 244 #We must create a file that we can access for later use
245 idLOCGPL <- genena %>% 245 idLOCGPL <- genena %>%
246 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>% 246 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
247 t(.) %>% 247 t(.) %>%
248 .[1,] %>% 248 .[1,] %>%
249 grep("^ID\\s*$",.) %>% 249 grep("^ID\\s*$",.) %>%
250 -1 250 -1
251 Firstval <- cbind(as.integer(gplnum),as.integer(idLOCGPL)) 251 Firstval <- cbind(as.integer(gplnum),as.integer(idLOCGPL))
252 colnames(Firstval) <- c("GPL_FILE_NUM","LOC_ID") 252 colnames(Firstval) <- c("GPL_FILE_NUM","LOC_ID")
253 write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE) 253 write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE)
254 geneIDNam <- genena %>% 254 geneIDNam <- genena %>%
255 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% 255 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
256 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.))) 256 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
257 } 257 }
258 } 258 }
259 if(soft == FALSE){ 259 if(soft == FALSE){
260 geneIDNam <- genena %>% 260 geneIDNam <- genena %>%
261 read_delim(delim="\t",comment = "#")%>% 261 read_delim(delim="\t",comment = "#")%>%
262 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.))) 262 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
263 } 263 }
264 264
265 ##Labeling the gene IDs without names 265 ##Labeling the gene IDs without names
266 geneIDNam <- NAFIXING(geneIDNam) 266 geneIDNam <- NAFIXING(geneIDNam)
267 267
268 ##remove the whitespace 268 ##remove the whitespace
269 geneIDNam <- t(rbind(str_trim(t(geneIDNam)[1,]),str_trim(t(geneIDNam)[2,]))) 269 geneIDNam <- t(rbind(str_trim(t(geneIDNam)[1,]),str_trim(t(geneIDNam)[2,])))
270 270
271 ##Here is the clean version 271 ##Here is the clean version
272 write.table(geneIDNam,file = paste0("Clean_GPL",gplnum,".txt"),sep = "\t",row.names = FALSE, col.names = FALSE) 272 write.table(geneIDNam,file = paste0("Clean_GPL",gplnum,".txt"),sep = "\t",row.names = FALSE, col.names = FALSE)
273 } 273 }
274 274
275 275
276 276
277 ##Changing the gene ID to gene name 277 ##Changing the gene ID to gene name
278 ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat)) 278 ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat))
279 colnames(ALZDAT) = ALZDAT1[1,] 279 colnames(ALZDAT) = ALZDAT1[1,]
280 280
281 281
282 ##Adjusting the column names aka the gene names 282 ##Adjusting the column names aka the gene names
283 colnames(ALZDAT) <- gcnames(ALZDAT) 283 colnames(ALZDAT) <- gcnames(ALZDAT)
284 284
285 285
286 #Full Data 286 #Full Data
287 Fullalzdw <- ALZDAT %>% 287 Fullalzdw <- ALZDAT %>%
288 as.data.frame() %>% 288 as.data.frame() %>%
289 cbind(ALZWORDF,.) 289 cbind(ALZWORDF,.)
290 290
291 291
292 #nfna <- strsplit(alz,"[\\|/]") %>% 292 #nfna <- strsplit(alz,"[\\|/]") %>%
293 # .[[1]] %>% 293 # .[[1]] %>%
294 # .[length(.)] %>% 294 # .[length(.)] %>%
295 # gsub("\\D","",.) %>% 295 # gsub("\\D","",.) %>%
296 # c("GSE",.,"after.txt") %>% 296 # c("GSE",.,"after.txt") %>%
297 # paste(collapse = "") 297 # paste(collapse = "")
298 #write.matrix(Fullalzdw,file = nfna,sep = "\t") 298 #write.matrix(Fullalzdw,file = nfna,sep = "\t")
299 299
300 #Perfect for excel viewing 300 #Perfect for excel viewing
301 nfnaex <- strsplit(alz,"[\\]") %>% 301 nfnaex <- strsplit(alz,"[\\]") %>%
302 .[[1]] %>% 302 .[[1]] %>%
303 .[length(.)] %>% 303 .[length(.)] %>%
304 gsub("\\D","",.) %>% 304 gsub("\\D","",.) %>%
305 c("GSE",.,"aftexcel.txt") %>% 305 c("GSE",.,"aftexcel.txt") %>%
306 paste(collapse = "") 306 paste(collapse = "")
307 write.table(t(Fullalzdw), file = nfnaex, sep = "\t") 307 write.table(t(Fullalzdw), file = nfnaex, sep = "\t")
308 308
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313 313