Commit da758df454781c9b5a48d30b9aaf7c8e4e994cf5
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b8bafad302
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Updated outputting new file: average before z-score
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RCleanDscret.R
| ... | ... | @@ -400,26 +400,47 @@ for(j in 1:length(tabRDATID)){ |
| 400 | 400 | j <- j + 1 |
| 401 | 401 | } |
| 402 | 402 | |
| 403 | -##Scaling the Data | |
| 404 | -scrawdat <- NuRDATN%>% | |
| 405 | - scale() | |
| 406 | -attr(scrawdat,"scaled:center") <- NULL | |
| 407 | -attr(scrawdat,"scaled:scale") <- NULL | |
| 408 | -colnames(scrawdat) <- rownames(tabRDATID) | |
| 409 | - | |
| 410 | -#Outputting the Z-score file | |
| 411 | -nfnzsc <- strsplit(alz,"[\\]") %>% | |
| 412 | - .[[1]] %>% | |
| 413 | - .[length(.)] %>% | |
| 414 | - gsub("\\D","",.) %>% | |
| 415 | - c("GSE",.,"zscore.txt") %>% | |
| 416 | - paste(collapse = "") | |
| 417 | -zscraw <- scrawdat %>% | |
| 418 | - t()%>% | |
| 419 | - as.data.frame(.,stringsAsFactors = FALSE) | |
| 420 | -colnames(zscraw) <- subjnam | |
| 421 | -write.table(zscraw, file = nfnzsc, sep = "\t",col.names = TRUE,row.names = TRUE) | |
| 422 | - | |
| 403 | +##Outputting non Z-score Average over genes | |
| 404 | + newoutput <-NuRDATN | |
| 405 | + colnames(newoutput) <- rownames(tabRDATID) | |
| 406 | + nfnewout <- strsplit(alz,"[\\]") %>% | |
| 407 | + .[[1]] %>% | |
| 408 | + .[length(.)] %>% | |
| 409 | + gsub("\\D","",.) %>% | |
| 410 | + c("GSE",.,"avg.txt") %>% | |
| 411 | + paste(collapse = "") | |
| 412 | + noutput <- newoutput %>% | |
| 413 | + t()%>% | |
| 414 | + as.data.frame(.,stringsAsFactors = FALSE) | |
| 415 | + noutput <- cbind(rownames(noutput),noutput) | |
| 416 | + colnames(noutput) <- c("Gene Symbol",subjnam) | |
| 417 | + rownames(noutput) <- NULL | |
| 418 | + write.table(noutput, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 419 | + | |
| 420 | + | |
| 421 | + ##Scaling the Data | |
| 422 | + scrawdat <- NuRDATN%>% | |
| 423 | + scale() | |
| 424 | + attr(scrawdat,"scaled:center") <- NULL | |
| 425 | + attr(scrawdat,"scaled:scale") <- NULL | |
| 426 | + colnames(scrawdat) <- rownames(tabRDATID) | |
| 427 | + | |
| 428 | + #Outputting the Z-score file | |
| 429 | + nfnzsc <- strsplit(alz,"[\\]") %>% | |
| 430 | + .[[1]] %>% | |
| 431 | + .[length(.)] %>% | |
| 432 | + gsub("\\D","",.) %>% | |
| 433 | + c("GSE",.,"zscore.txt") %>% | |
| 434 | + paste(collapse = "") | |
| 435 | + zscraw <- scrawdat %>% | |
| 436 | + t()%>% | |
| 437 | + as.data.frame(.,stringsAsFactors = FALSE) | |
| 438 | + zscraw <- cbind(rownames(zscraw),zscraw) | |
| 439 | + colnames(zscraw) <- c("Gene Symbol",subjnam) | |
| 440 | + rownames(zscraw) <- NULL | |
| 441 | + write.table(zscraw, file = nfnewout, sep = "\t",col.names = TRUE,row.names = FALSE) | |
| 442 | + | |
| 443 | + | |
| 423 | 444 | ##Discretized the Data |
| 424 | 445 | dialzdat <- scrawdat %>% |
| 425 | 446 | dndat(.) %>% |