# #——风格,eval = TRUE,呼应= FALSE,结果= "飞机 "-------------------------- BiocStyle:乳胶 () ## ---- 标签=设置,呼应= FALSE, eval = TRUE——选项(宽度= 55)# #标签= loadpackage呼应= TRUE, eval = TRUE,结果=“隐藏”,消息= FALSE——图书馆(compcodeR) # #标签= simulatedata呼应= TRUE, eval = FALSE,整洁= FALSE——# B_625_625 < - generateSyntheticData(数据集=“B_625_625 n.vars = 12500, # samples.per.cond = 5, n.diffexp = 1250, # repl。Id = 1, seqdepth = 1e7， # fraction。u= 0.5， # between.group.diffdisp = FALSE， # filter.threshold.total = 1， # filter.threshold.mediancpm = 0， # fraction.non. overscattering = 0， # output. filter = 0。(B_625_625_5spc_repl1.rds) ## ----label = reportsimulate, echo = TRUE, eval = FALSE, tidy = FALSE---- # summarizeSyntheticDataSet(数据。set = "B_625_625_5spc_repl1. "Rds”，#输出。文件名= " b_625_625_5spc_repl1_datachheck .html") ## ----label = rundiffexp1, echo = TRUE, eval = FALSE, tidy = FALSE---- # runDiffExp(data. exe)file = "B_625_625_5spc_repl1. "Rds”，#结果。Extent = " boom . "limma"， Rmdfunction = " vom .limma. "createRmd”，#输出。Directory = "."， norm。runDiffExp(data. method = "TMM")file = "B_625_625_5spc_repl1. "Rds”，#结果。extent = "edgeR. "， Rmdfunction = "edgeR.exact. "createRmd”，#输出。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())