Efrain Gonzalez / Cleaning and Fixing Data with R

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Commit 6a66705877a70dd83cb8cff53f5b52f447b4dc76

Authored by Efrain Gonzalez
1 parent 769f081f9b
Exists in master

Don't use this code yet 

updated else if statements
Showing 1 changed file with 20 additions and 38 deletions   Show diff stats
... ... @@ -27,11 +27,9 @@ chngrownm <- function(mat){
27 27 for(e in 1:col){
28 28 if("!Sample_source_name_ch1"==mat[1,e]){
29 29 colnames(mat)[e] <- "Brain_Region"
30   - }
31   - else if("!Sample_title" == mat[1,e]){
  30 + } else if("!Sample_title" == mat[1,e]){
32 31 colnames(mat)[e] <- "Title"
33   - }
34   - else if("!Sample_geo_accession" == mat[1,e]){
  32 + } else if("!Sample_geo_accession" == mat[1,e]){
35 33 colnames(mat)[e] <- "ID_REF"
36 34 } else{
37 35 if(grepl("Sex|gender|Gender|sex",mat[2,e])==TRUE){
... ... @@ -68,19 +66,15 @@ cinfo &lt;- function(mat){
68 66 for(j in 2:col){
69 67 if(grepl("Group",colnames(mat)[j]) == TRUE){
70 68 mat[,j] <- gsub(".+:\\s|\\s.+;.+","",mat[,j])
71   - }
72   - else if(grepl("Age",colnames(mat)[j])==TRUE){
  69 + } else if(grepl("Age",colnames(mat)[j])==TRUE){
73 70 mat[,j] <- gsub("\\D","",mat[,j])%>%
74 71 as.integer()
75   - }
76   - else if(grepl("Sex",colnames(mat)[j])==TRUE){
  72 + } else if(grepl("Sex",colnames(mat)[j])==TRUE){
77 73 mat[,j] <- gsub(".+:\\s","",mat[,j])
78   - }
79   - else if(grepl("PMI",colnames(mat)[j])==TRUE){
  74 + } else if(grepl("PMI",colnames(mat)[j])==TRUE){
80 75 mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>%
81 76 as.numeric()
82   - }
83   - else if(grepl("Braak",colnames(mat)[j])==TRUE){
  77 + } else if(grepl("Braak",colnames(mat)[j])==TRUE){
84 78 mat[,j]<-gsub(".+:\\s","",mat[,j])%>%
85 79 as.roman()%>%
86 80 as.integer()
... ... @@ -168,11 +162,9 @@ dndat &lt;- function(NDATA){
168 162  
169 163 if(NDATA[i,j] < -1){
170 164 DDATA[i,j]=0L
171   - }
172   - else if(NDATA[i,j] > 1){
  165 + } else if(NDATA[i,j] > 1){
173 166 DDATA[i,j]=2L
174   - }
175   - else if(-1 <= NDATA[i,j] && NDATA[i,j] < 1){
  167 + } else if(-1 <= NDATA[i,j] && NDATA[i,j] < 1){
176 168 DDATA[i,j]=1L
177 169 }
178 170 } else{
... ... @@ -276,8 +268,7 @@ THEFT &lt;- function(){
276 268 geneIDNam <- genena %>%
277 269 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
278 270 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
279   - }
280   - else if(IDF == 0){
  271 + } else if(IDF == 0){
281 272 #No information on this particular GPL file
282 273 idLOCGPL <- genena %>%
283 274 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -290,8 +281,7 @@ THEFT &lt;- function(){
290 281 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
291 282 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
292 283 }
293   - }
294   - else if(fileex == 0){
  284 + } else if(fileex == 0){
295 285 #We must create a file that we can access for later use
296 286 idLOCGPL <- genena %>%
297 287 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -305,8 +295,7 @@ THEFT &lt;- function(){
305 295 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
306 296 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
307 297 }
308   - }
309   - else if(soft == FALSE){
  298 + } else if(soft == FALSE){
310 299 geneIDNam <- genena %>%
311 300 read_delim(delim="\t",comment = "#")%>%
312 301 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
... ... @@ -407,9 +396,8 @@ THEFT &lt;- function(){
407 396 ##Putting the ones without duplicates in their new homes
408 397 if(tabRDATID[j] == 1){
409 398 NuRDATN[,j] <- RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])]
410   - }
411   - ##Averaging duplicates and putting them in their new homes
412   - else if(tabRDATID[j] > 1){
  399 + } else if(tabRDATID[j] > 1){
  400 + ##Averaging duplicates and putting them in their new homes
413 401 NuRDATN[,j] <- rowMeans(RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])],na.rm = TRUE)
414 402 }
415 403 j <- j + 1
... ... @@ -476,10 +464,9 @@ THEFT &lt;- function(){
476 464 write.table(Dscrtalzdw, file = nfnaex2, sep = "\t",col.names = TRUE,row.names = FALSE)
477 465 n <- n +1
478 466 }
479   - }
480   -
  467 + } else if(numDAT == 2){
481 468 #CHOOSE A DATA FILE TO CLEAN OR SEVERAL DATA FILES TO CLEAN
482   - else if(numDAT == 2){
  469 +
483 470 #All the files you want to analyze
484 471 ANDIS <- select.list(choices = list.files()[GSEfileloc],multiple = TRUE, title = "Choose the file/files you want to analyze:")
485 472 if(length(ANDIS) == 0){
... ... @@ -541,8 +528,7 @@ THEFT &lt;- function(){
541 528 geneIDNam <- paste0("Clean_GPL",gplnum,".txt") %>%
542 529 read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
543 530  
544   - }
545   - else if(clfileex == 0){
  531 + } else if(clfileex == 0){
546 532 ##Lets Create a clean version
547 533  
548 534 ##Gene ID to Gene Name
... ... @@ -565,8 +551,7 @@ THEFT &lt;- function(){
565 551 geneIDNam <- genena %>%
566 552 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
567 553 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
568   - }
569   - else if(IDF == 0){
  554 + } else if(IDF == 0){
570 555 #No information on this particular GPL file
571 556 idLOCGPL <- genena %>%
572 557 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -579,8 +564,7 @@ THEFT &lt;- function(){
579 564 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
580 565 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
581 566 }
582   - }
583   - else if(fileex == 0){
  567 + } else if(fileex == 0){
584 568 #We must create a file that we can access for later use
585 569 idLOCGPL <- genena %>%
586 570 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -594,8 +578,7 @@ THEFT &lt;- function(){
594 578 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>%
595 579 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
596 580 }
597   - }
598   - else if(soft == FALSE){
  581 + } else if(soft == FALSE){
599 582 geneIDNam <- genena %>%
600 583 read_delim(delim="\t",comment = "#")%>%
601 584 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
... ... @@ -696,9 +679,8 @@ THEFT &lt;- function(){
696 679 ##Putting the ones without duplicates in their new homes
697 680 if(tabRDATID[j] == 1){
698 681 NuRDATN[,j] <- RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])]
699   - }
  682 + } else if(tabRDATID[j] > 1){
700 683 ##Averaging duplicates and putting them in their new homes
701   - else if(tabRDATID[j] > 1){
702 684 NuRDATN[,j] <- rowMeans(RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])],na.rm = TRUE)
703 685 }
704 686 j <- j + 1