################################################### ### chunk number 1: setup1 ################################################### #line 77 "vignettes/RNAither/inst/doc/vignetteRNAither.Rnw" library("RNAither") ################################################### ### chunk number 2: ################################################### #line 81 "vignettes/RNAither/inst/doc/vignetteRNAither.Rnw" #gene names plateLayout1 <- c("test1", "empty", "test3", "test4", "test5", "test6", "test7", "empty", "test9", "test10", "test11", "test12") plateLayout2 <- c("test1", "test2", "test3", "test4", "test5", "test6", "test7", "test8", "test9", "test10", "test11", "test12") plateLayout <- cbind(plateLayout1, plateLayout2) emptyWells <- list(c(2, 8), NA_integer_) #the first plate has two empty wells at position 2 and 8, #the second plate does not have any empty wells poorWells <- NA_integer_ #no wells of poor quality controlCoordsOutput <- list(list(NA_integer_, NA_integer_), list(NA_integer_, c(9,10))) #the first plate does not have any control siRNAs, #the second plate has two negative controls at position 9 and 10 backgroundValOutput<-NA_integer_ #no background signal intensities available sigPlate1<-c(2578, NA_integer_, 3784, 3784, 2578, 5555, 5555, NA_integer_, 8154, 2578, 3784, 2578) sigPlate2<-c(8154, 3784, 5555, 3784, 11969, 2578, 1196, 5555, 17568, 2578, 5555, 2578) #the signal intensities on the plates meanSignalOutput<-list(sigPlate1, sigPlate2) SDmeansignal<-NA_integer_ #no standard deviation available objnumOutput<-NA_integer_ #no cell count available cellnumOutput<-NA_integer_ generateDatasetFile("First test screen", "RNAi in virus-infected cells", NA_character_, "testscreen_output.txt", plateLayout, plateLayout, 3, 4, 1, emptyWells, poorWells, controlCoordsOutput, backgroundValOutput, meanSignalOutput, SDmeansignal, objnumOutput, cellnumOutput) #load the dataset into R: header<-readLines("testscreen_output.txt",3) dataset<-read.table("testscreen_output.txt", skip=3, colClasses=c(NA, NA, NA, NA, "factor", NA, NA, NA, NA, NA, NA, NA, NA, NA), stringsAsFactors=FALSE) ################################################### ### chunk number 3: ################################################### #line 133 "vignettes/RNAither/inst/doc/vignetteRNAither.Rnw" data(exampleDataset, package="RNAither") doubledataset <- joinDatasets(list(dataset, dataset)) ################################################### ### chunk number 4: ################################################### #line 140 "vignettes/RNAither/inst/doc/vignetteRNAither.Rnw" data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") saveDataset(header, dataset, "save_testfile1.txt") header[[1]] <- "external_experiment_name,Test screen" header[[2]] <- "comments,contains twice Screen Nb. 1" joinDatasetFiles(list( "save_testfile1.txt", "save_testfile1.txt"), 3, header, "concatenated_testfile.txt")