## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----label = settings, echo = FALSE, eval = TRUE----- options(width = 55) ## ----label = loadpackage, echo = TRUE, eval = TRUE, results = 'hide', message = FALSE---- library(compcodeR) ## ----label = simulatedata, echo = TRUE, eval = FALSE, tidy = FALSE---- # B_625_625 <- generateSyntheticData(dataset = "B_625_625", n.vars = 12500, # samples.per.cond = 5, n.diffexp = 1250, # repl.id = 1, seqdepth = 1e7, # fraction.upregulated = 0.5, # between.group.diffdisp = FALSE, # filter.threshold.total = 1, # filter.threshold.mediancpm = 0, # fraction.non.overdispersed = 0, # output.file = "B_625_625_5spc_repl1.rds") ## ----label = reportsimulated, echo = TRUE, eval = FALSE, tidy = FALSE---- # summarizeSyntheticDataSet(data.set = "B_625_625_5spc_repl1.rds", # output.filename = "B_625_625_5spc_repl1_datacheck.html") ## ----label = rundiffexp1, echo = TRUE, eval = FALSE, tidy = FALSE---- # runDiffExp(data.file = "B_625_625_5spc_repl1.rds", # result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", # output.directory = ".", norm.method = "TMM") # runDiffExp(data.file = "B_625_625_5spc_repl1.rds", # result.extent = "edgeR.exact", Rmdfunction = "edgeR.exact.createRmd", # output.directory = ".", norm.method = "TMM", # trend.method = "movingave", disp.type = "tagwise") # runDiffExp(data.file = "B_625_625_5spc_repl1.rds", result.extent = "ttest", # Rmdfunction = "ttest.createRmd", # output.directory = ".", norm.method = "TMM") ## ----label = listcreatermd, echo = TRUE, eval = TRUE---- listcreateRmd() ## ----label = runcomparison, echo = TRUE, eval = FALSE, tidy = FALSE---- # runComparisonGUI(input.directories = ".", # output.directory = ".", recursive = FALSE) ## ----label = generatecode, echo = TRUE, eval = FALSE---- # generateCodeHTMLs("B_625_625_5spc_repl1_ttest.rds", ".") ## ----label = nogui-comparison, echo = TRUE, eval = FALSE, tidy = FALSE---- # file.table <- data.frame(input.files = c("B_625_625_5spc_repl1_voom.limma.rds", # "B_625_625_5spc_repl1_ttest.rds", # "B_625_625_5spc_repl1_edgeR.exact.rds"), # stringsAsFactors = FALSE) # parameters <- list(incl.nbr.samples = NULL, incl.replicates = NULL, # incl.dataset = "B_625_625", incl.de.methods = NULL, # fdr.threshold = 0.05, tpr.threshold = 0.05, # typeI.threshold = 0.05, ma.threshold = 0.05, # fdc.maxvar = 1500, overlap.threshold = 0.05, # fracsign.threshold = 0.05, # comparisons = c("auc", "fdr", "tpr", "ma", "correlation")) # runComparison(file.table = file.table, parameters = parameters, output.directory = ".") ## ----create-compData, eval = TRUE, tidy = FALSE------ count.matrix <- matrix(round(1000*runif(4000)), 1000, 4) sample.annot <- data.frame(condition = c(1, 1, 2, 2)) info.parameters <- list(dataset = "mytestdata", uID = "123456") cpd <- compData(count.matrix = count.matrix, sample.annotations = sample.annot, info.parameters = info.parameters) check_compData(cpd) ## ----label = savedata, echo = TRUE, eval = FALSE----- # saveRDS(cpd, "saveddata.rds") ## ----session-info, eval = TRUE, echo = FALSE, results="asis"---- toLatex(sessionInfo())