Commit b8bafad302138b13b3381aa768c2fe29142fa42c
1 parent
1b7f1377e8
Exists in
master
Updated by adding in output for average without zscore
Showing
1 changed file
with
66 additions
and
24 deletions
Show diff stats
RAutoClDs.R
| ... | ... | @@ -404,7 +404,26 @@ THEFT <- function(){ |
| 404 | 404 | } |
| 405 | 405 | j <- j + 1 |
| 406 | 406 | } |
| 407 | - | |
| 407 | + | |
| 408 | + | |
| 409 | + ##Outputting non Z-score Average over genes | |
| 410 | + newoutput <-NuRDATN | |
| 411 | + colnames(newoutput) <- rownames(tabRDATID) | |
| 412 | + nfnewout <- strsplit(alz,"[\\]") %>% | |
| 413 | + .[[1]] %>% | |
| 414 | + .[length(.)] %>% | |
| 415 | + gsub("\\D","",.) %>% | |
| 416 | + c("GSE",.,"newout.txt") %>% | |
| 417 | + paste(collapse = "") | |
| 418 | + noutput <- newoutput %>% | |
| 419 | + t()%>% | |
| 420 | + as.data.frame(.,stringsAsFactors = FALSE) | |
| 421 | + noutput <- cbind(rownames(noutput),noutput) | |
| 422 | + colnames(noutput) <- c("Gene Symbol",subjnam) | |
| 423 | + rownames(noutput) <- NULL | |
| 424 | + write.table(noutput, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 425 | + | |
| 426 | + | |
| 408 | 427 | ##Scaling the Data |
| 409 | 428 | scrawdat <- NuRDATN%>% |
| 410 | 429 | scale() |
| ... | ... | @@ -417,14 +436,17 @@ THEFT <- function(){ |
| 417 | 436 | .[[1]] %>% |
| 418 | 437 | .[length(.)] %>% |
| 419 | 438 | gsub("\\D","",.) %>% |
| 420 | - c("GSE",.,"zscore.txt") %>% | |
| 439 | + c("GSE",.,"avg.txt") %>% | |
| 421 | 440 | paste(collapse = "") |
| 422 | 441 | zscraw <- scrawdat %>% |
| 423 | 442 | t()%>% |
| 424 | 443 | as.data.frame(.,stringsAsFactors = FALSE) |
| 425 | - colnames(zscraw) <- subjnam | |
| 426 | - write.table(zscraw, file = nfnzsc, sep = "\t",col.names = TRUE,row.names = TRUE) | |
| 427 | - | |
| 444 | + zscraw <- cbind(rownames(zscraw),zscraw) | |
| 445 | + colnames(zscraw) <- c("Gene Symbol",subjnam) | |
| 446 | + rownames(zscraw) <- NULL | |
| 447 | + write.table(zscraw, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 448 | + | |
| 449 | + | |
| 428 | 450 | ##Discretized the Data |
| 429 | 451 | dialzdat <- scrawdat %>% |
| 430 | 452 | dndat(.) %>% |
| ... | ... | @@ -706,25 +728,45 @@ THEFT <- function(){ |
| 706 | 728 | j <- j + 1 |
| 707 | 729 | } |
| 708 | 730 | |
| 709 | - ##Scaling the Data | |
| 710 | - scrawdat <- NuRDATN%>% | |
| 711 | - scale() | |
| 712 | - attr(scrawdat,"scaled:center") <- NULL | |
| 713 | - attr(scrawdat,"scaled:scale") <- NULL | |
| 714 | - colnames(scrawdat) <- rownames(tabRDATID) | |
| 715 | - | |
| 716 | - #Outputting the Z-score file | |
| 717 | - nfnzsc <- strsplit(alz,"[\\]") %>% | |
| 718 | - .[[1]] %>% | |
| 719 | - .[length(.)] %>% | |
| 720 | - gsub("\\D","",.) %>% | |
| 721 | - c("GSE",.,"zscore.txt") %>% | |
| 722 | - paste(collapse = "") | |
| 723 | - zscraw <- scrawdat %>% | |
| 724 | - t()%>% | |
| 725 | - as.data.frame(.,stringsAsFactors = FALSE) | |
| 726 | - colnames(zscraw) <- subjnam | |
| 727 | - write.table(zscraw, file = nfnzsc, sep = "\t",col.names = TRUE,row.names = TRUE) | |
| 731 | + ##Outputting non Z-score Average over genes | |
| 732 | + newoutput <-NuRDATN | |
| 733 | + colnames(newoutput) <- rownames(tabRDATID) | |
| 734 | + nfnewout <- strsplit(alz,"[\\]") %>% | |
| 735 | + .[[1]] %>% | |
| 736 | + .[length(.)] %>% | |
| 737 | + gsub("\\D","",.) %>% | |
| 738 | + c("GSE",.,"avg.txt") %>% | |
| 739 | + paste(collapse = "") | |
| 740 | + noutput <- newoutput %>% | |
| 741 | + t()%>% | |
| 742 | + as.data.frame(.,stringsAsFactors = FALSE) | |
| 743 | + noutput <- cbind(rownames(noutput),noutput) | |
| 744 | + colnames(noutput) <- c("Gene Symbol",subjnam) | |
| 745 | + rownames(noutput) <- NULL | |
| 746 | + write.table(noutput, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 747 | + | |
| 748 | + | |
| 749 | + ##Scaling the Data | |
| 750 | + scrawdat <- NuRDATN%>% | |
| 751 | + scale() | |
| 752 | + attr(scrawdat,"scaled:center") <- NULL | |
| 753 | + attr(scrawdat,"scaled:scale") <- NULL | |
| 754 | + colnames(scrawdat) <- rownames(tabRDATID) | |
| 755 | + | |
| 756 | + #Outputting the Z-score file | |
| 757 | + nfnzsc <- strsplit(alz,"[\\]") %>% | |
| 758 | + .[[1]] %>% | |
| 759 | + .[length(.)] %>% | |
| 760 | + gsub("\\D","",.) %>% | |
| 761 | + c("GSE",.,"zscore.txt") %>% | |
| 762 | + paste(collapse = "") | |
| 763 | + zscraw <- scrawdat %>% | |
| 764 | + t()%>% | |
| 765 | + as.data.frame(.,stringsAsFactors = FALSE) | |
| 766 | + zscraw <- cbind(rownames(zscraw),zscraw) | |
| 767 | + colnames(zscraw) <- c("Gene Symbol",subjnam) | |
| 768 | + rownames(zscraw) <- NULL | |
| 769 | + write.table(zscraw, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 728 | 770 | |
| 729 | 771 | ##Discretized the Data |
| 730 | 772 | dialzdat <- scrawdat %>% |