Commit 77a0d64ff05e500f7e8ce62ee77861c5ec72b0b3
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7f2b84c8cf
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master
Updated: Added |^GENE_SYMBOL$ to glossary
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RAutoClDs.R
... | ... | @@ -264,7 +264,7 @@ THEFT <- function(){ |
264 | 264 | .[IDLOCAL] |
265 | 265 | geneIDNam <- genena %>% |
266 | 266 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>% |
267 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
267 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
268 | 268 | } else if(IDF == 0){ |
269 | 269 | #No information on this particular GPL file |
270 | 270 | idLOCGPL <- genena %>% |
... | ... | @@ -276,7 +276,7 @@ THEFT <- function(){ |
276 | 276 | cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE) |
277 | 277 | geneIDNam <- genena %>% |
278 | 278 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% |
279 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
279 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
280 | 280 | } |
281 | 281 | } else if(fileex == 0){ |
282 | 282 | #We must create a file that we can access for later use |
... | ... | @@ -290,12 +290,12 @@ THEFT <- function(){ |
290 | 290 | write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE) |
291 | 291 | geneIDNam <- genena %>% |
292 | 292 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% |
293 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
293 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
294 | 294 | } |
295 | 295 | } else if(soft == FALSE){ |
296 | 296 | geneIDNam <- genena %>% |
297 | 297 | read_delim(delim="\t",comment = "#")%>% |
298 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
298 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
299 | 299 | } |
300 | 300 | |
301 | 301 | ##Labeling the gene IDs without names |
... | ... | @@ -565,7 +565,7 @@ THEFT <- function(){ |
565 | 565 | .[IDLOCAL] |
566 | 566 | geneIDNam <- genena %>% |
567 | 567 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idlocgpl) %>% |
568 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
568 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
569 | 569 | } else if(IDF == 0){ |
570 | 570 | #No information on this particular GPL file |
571 | 571 | idLOCGPL <- genena %>% |
... | ... | @@ -577,7 +577,7 @@ THEFT <- function(){ |
577 | 577 | cat(file="GPL_ID_LOC.txt",sep = "\t", fill = TRUE, append = TRUE) |
578 | 578 | geneIDNam <- genena %>% |
579 | 579 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% |
580 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
580 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
581 | 581 | } |
582 | 582 | } else if(fileex == 0){ |
583 | 583 | #We must create a file that we can access for later use |
... | ... | @@ -591,12 +591,12 @@ THEFT <- function(){ |
591 | 591 | write.table(Firstval,file = "GPL_ID_LOC.txt", sep = "\t",row.names = FALSE, col.names = TRUE) |
592 | 592 | geneIDNam <- genena %>% |
593 | 593 | read_delim(delim="\t",col_names = TRUE, comment = "!", skip = idLOCGPL) %>% |
594 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
594 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
595 | 595 | } |
596 | 596 | } else if(soft == FALSE){ |
597 | 597 | geneIDNam <- genena %>% |
598 | 598 | read_delim(delim="\t",comment = "#")%>% |
599 | - dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$",colnames(.))) | |
599 | + dplyr::select(.,ID,grep("Symbol|^ORF\\s*$|^gene_assignment\\s*$|^Gene symbol$|^GENE_SYMBOL$",colnames(.))) | |
600 | 600 | } |
601 | 601 | |
602 | 602 | ##Labeling the gene IDs without names |