Efrain Gonzalez / Cleaning and Fixing Data with R

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Commit 8953eaff1bf653b09805a78ffb84c4aa0b4699e7

Authored by Efrain Gonzalez
1 parent 6a58f94d23
Exists in master

Don't use this code 

changed more ifs to else ifs
Showing 1 changed file with 11 additions and 11 deletions   Show diff stats
... ... @@ -235,7 +235,7 @@ THEFT <- function(){
235 235 read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
236 236  
237 237 }
238   - if(clfileex == 0){
  238 + else if(clfileex == 0){
239 239 ##Lets Create a clean version
240 240  
241 241 ##Gene ID to Gene Name
... ... @@ -259,7 +259,7 @@ THEFT <- function(){
259 259 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
260 260 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
261 261 }
262   - if(IDF == 0){
  262 + else if(IDF == 0){
263 263 #No information on this particular GPL file
264 264 idLOCGPL <- genena %>%
265 265 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -273,7 +273,7 @@ THEFT &lt;- function(){
273 273 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
274 274 }
275 275 }
276   - if(fileex == 0){
  276 + else if(fileex == 0){
277 277 #We must create a file that we can access for later use
278 278 idLOCGPL <- genena %>%
279 279 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -288,7 +288,7 @@ THEFT &lt;- function(){
288 288 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
289 289 }
290 290 }
291   - if(soft == FALSE){
  291 + else if(soft == FALSE){
292 292 geneIDNam <- genena %>%
293 293 read_delim(delim="\t",comment = "#")%>%
294 294 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
... ... @@ -391,7 +391,7 @@ THEFT &lt;- function(){
391 391 NuRDATN[,j] <- RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])]
392 392 }
393 393 ##Averaging duplicates and putting them in their new homes
394   - if(tabRDATID[j] > 1){
  394 + else if(tabRDATID[j] > 1){
395 395 NuRDATN[,j] <- rowMeans(RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])],na.rm = TRUE)
396 396 }
397 397 j <- j + 1
... ... @@ -461,7 +461,7 @@ THEFT &lt;- function(){
461 461 }
462 462  
463 463 #CHOOSE A DATA FILE TO CLEAN OR SEVERAL DATA FILES TO CLEAN
464   - if(numDAT == 2){
  464 + else if(numDAT == 2){
465 465 #All the files you want to analyze
466 466 ANDIS <- select.list(choices = list.files()[GSEfileloc],multiple = TRUE, title = "Choose the file/files you want to analyze:")
467 467 if(length(ANDIS) == 0){
... ... @@ -524,7 +524,7 @@ THEFT &lt;- function(){
524 524 read_delim(delim="\t",col_names = c("ID","Symbol"), comment = "!")
525 525  
526 526 }
527   - if(clfileex == 0){
  527 + else if(clfileex == 0){
528 528 ##Lets Create a clean version
529 529  
530 530 ##Gene ID to Gene Name
... ... @@ -548,7 +548,7 @@ THEFT &lt;- function(){
548 548 read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>%
549 549 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
550 550 }
551   - if(IDF == 0){
  551 + else if(IDF == 0){
552 552 #No information on this particular GPL file
553 553 idLOCGPL <- genena %>%
554 554 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -562,7 +562,7 @@ THEFT &lt;- function(){
562 562 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
563 563 }
564 564 }
565   - if(fileex == 0){
  565 + else if(fileex == 0){
566 566 #We must create a file that we can access for later use
567 567 idLOCGPL <- genena %>%
568 568 read_delim(delim="\t",col_names = FALSE, comment = "!", n_max = 1000) %>%
... ... @@ -577,7 +577,7 @@ THEFT &lt;- function(){
577 577 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
578 578 }
579 579 }
580   - if(soft == FALSE){
  580 + else if(soft == FALSE){
581 581 geneIDNam <- genena %>%
582 582 read_delim(delim="\t",comment = "#")%>%
583 583 dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$",colnames(.)))
... ... @@ -680,7 +680,7 @@ THEFT &lt;- function(){
680 680 NuRDATN[,j] <- RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])]
681 681 }
682 682 ##Averaging duplicates and putting them in their new homes
683   - if(tabRDATID[j] > 1){
  683 + else if(tabRDATID[j] > 1){
684 684 NuRDATN[,j] <- rowMeans(RAWDATNUM[,which(RAWDATID==rownames(tabRDATID)[j])],na.rm = TRUE)
685 685 }
686 686 j <- j + 1