Efrain Gonzalez / Cleaning and Fixing Data with R

Download as
Browse Code ยป

Commit cc59b7f8323cecc33ca1facf20f024c2a1b5a73e

Authored by Efrain Gonzalez
1 parent c0625ba184
Exists in master

Second version of code (UNTESTED)

Showing 1 changed file with 284 additions and 0 deletions   Show diff stats
File was created 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 x <- 1
92 for(i in 1:row){
93 if(grepl("^NA\\s*$",GIDNAM[i,2])==TRUE){
94 GIDNAM[i,2] <- gsub(".*",paste0(NA,x),GIDNAM[i,2])
95 x <- x + 1
96 }
97 i <- i + 1
98 }
99 GIDNAM
100 }
101
102 #4#Function for changing the gene ID to gene name
103 cgeneID <- function(GeneName,DATA){
104 colGene <- dim(GeneName)[2]
105 j <- 1
106 for(j in 1:colGene){
107 chngsreq <- grep(GeneName[1,j],DATA[1,])
108 DATA[1,chngsreq] <- gsub(GeneName[1,j],GeneName[2,j],DATA[1,chngsreq])
109 j = j+1
110 }
111 DATA
112 }
113
114 #5#Function for adjusting the gene names
115 gcnames <- function(DiData,usecol=1){
116 nuruns <- dim(DiData)[2]
117 i = 1
118 nwnam <- rep("0",length.out=nuruns)
119 for(i in 1:nuruns){
120 if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){
121 nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][usecol]
122 } else{
123 nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][1]
124 }
125
126 }
127 nwnam
128
129 }
130
131
132
133 #The Rest of this code will be used every time you want to change a data set
134
135 #Getting the series matrix file
136 print("Choose the series matrix file that you want to Analyze")
137 alz <- file.choose()
138
139 #Getting the GPL file
140 print("Choose the GPL file that correlates with the above series matrix file")
141 genena <- file.choose()
142
143
144 #Set working directory based on the directory of the series matrix file Currently only works for windows
145 ##strsplit(alz,"[\\]") %>%
146 ## .[[1]] %>%
147 ## .[-length(.)] %>%
148 ## paste(.,collapse="/") %>%
149 ## setwd()
150
151 #Find out if it is a soft GPL file or not
152 soft <- strsplit(genena,"[\\|/]") %>%
153 .[[1]] %>%
154 .[length(.)] %>%
155 grepl("soft",.)
156
157 #Working with the wordy part of the document
158 alzword <- alz %>%
159 read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>%
160 filter(grepl("!Sample",X1))%>%
161 filter(!grepl("!Sample_contact",X1))
162
163 ##Changing row names and column names:
164 ALZWORD <- t(alzword)
165 rownames(ALZWORD)=NULL
166 colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE)
167 ALZWORD <- chngrownm(ALZWORD)[-1,]
168 ALZWORD <- ALZWORD%>%
169 as.data.frame()%>%
170 dplyr::select(-starts_with("col"))
171
172 ##Reorganizing information within the columns
173 ALZWORDF <- cinfo(ALZWORD)
174
175
176 #Working with Actual Data part of file
177 alzdat <- alz %>%
178 read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1)
179 ALZDAT <- t(alzdat[,-1])
180 rownames(ALZDAT)=NULL
181
182
183 ##Gene ID to Gene Name
184 ###geneIDNam <- genena %>%
185 ### read_delim(delim="\t",comment = "#")%>%
186 ### dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
187 ###problems with the above for soft files
188 if(soft == TRUE){
189 gplnum <- strsplit(genena,"[\\|/]") %>%
190 .[[1]] %>%
191 .[length(.)] %>%
192 gsub("\\D","",.)
193 #Check to see if there is already a file containing information on soft files
194 fileex <- sum(grepl("GPL_ID_LOC.txt",list.files()))
195 if(fileex == 1){
196 #Check to see if this GPL soft file has been used before
197 IDF <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
198 .$GPL_FILE_NUM%>%
199 grepl(gplnum,.) %>%
200 sum()
201 if(IDF == 1){
202 IDLOCAL <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
203 .$GPL_FILE_NUM%>%
204 grep(gplnum,.)
205 idlocgpl <- read_delim("GPL_ID_LOC.txt",delim = "\t",col_names = TRUE) %>%
206 .$LOC_ID %>%
207 .[IDLOCAL]
208 geneIDNam <- genena %>%
209 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
210 dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
211 }
212 if(IDF == 0){
213 #No information on this particular GPL file
214 idLOCGPL <- genena %>%
215 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
216 t(.) %>%
217 grep("^\\D",.) %>%
218 length()-1
219 cbind(as.integer(gplnum),as.integer(idLOCGPL)) %>%
220 cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE)
221 geneIDNam <- genena %>%
222 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
223 dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
224 }
225 }
226 if(fileex == 0){
227 #We must create a file that we can access for later use
228 idLOCGPL <- genena %>%
229 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
230 t(.) %>%
231 grep("^\\D",.) %>%
232 length()-1
233 Firstval <- cbind(as.integer(gplnum),as.integer(idLOCGPL))
234 colnames(Firstval) <- c("GPL_FILE_NUM","LOC_ID")
235 write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE)
236 geneIDNam <- genena %>%
237 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
238 dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
239 }
240 }
241 if(soft == FALSE){
242 geneIDNam <- genena %>%
243 read_delim(delim="\t",comment = "#")%>%
244 dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
245 }
246
247 ##Labeling the gene IDs without names
248 geneIDNam <- NAFIXING(geneIDNam)
249
250 ##remove the whitespace
251 geneIDNam <- t(rbind(str_trim(t(geneIDNam)[1,]),str_trim(t(geneIDNam)[2,])))
252
253 ##Changing the gene ID to gene name
254 ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat))
255 colnames(ALZDAT) = ALZDAT1[1,]
256
257
258 ##Adjusting the column names aka the gene names
259 colnames(ALZDAT) <- gcnames(ALZDAT)
260
261
262 #Full Data
263 Fullalzdw <- ALZDAT %>%
264 as.data.frame() %>%
265 cbind(ALZWORDF,.)
266
267
268 nfna <- strsplit(alz,"[\\]") %>%
269 .[[1]] %>%
270 .[length(.)] %>%
271 gsub("\\D","",.) %>%
272 c("GSE",.,"after.txt") %>%
273 paste(collapse = "")
274 write.matrix(Fullalzdw,file = nfna,sep = "\t")
275 #Perfect for excel viewing
276 nfnaex <- strsplit(alz,"[\\]") %>%
277 .[[1]] %>%
278 .[length(.)] %>%
279 gsub("\\D","",.) %>%
280 c("GSE",.,"aftexcel.txt") %>%
281 paste(collapse = "")
282 write.table(t(Fullalzdw), file = nfnaex, sep = "\t")
283
284
285