# #——“installDer”,eval = FALSE ----------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) {# install.packages(“BiocManager ") # } # # (“derfinderHelper BiocManager:安装 ") # # ## 检查你有一个有效的Bioconductor安装# BiocManager::有效 () ## ----' 引用 '--------------------------------------------------------------- ## 引用信息的引用(“derfinderHelper ") ## ---- vignetteSetup回声= FALSE,消息= FALSE,警告= FALSE ---------------- ## 跟踪时间使装饰图案开始时间< - Sys.time() # #围嘴设置库(“RefManageR”)# #写书目信息围嘴< - c (derfinderHelper =引文(“derfinderHelper”)[1],BiocStyle =引文(“BiocStyle”),knitr =引文(“knitr”)[3],RefManageR =引文(“RefManageR”)[1],rmarkdown =引文(“rmarkdown”),R =引文(),IRanges =引文(“IRanges”),矩阵=引文(“矩阵”),S4Vectors = RefManageR:: BibEntry (bibtype =“手册”,key = "S4Vectors"， author = "Hervé Pagès and Michael Lawrence and Patrick Aboyoun"， title = "S4Vectors: S4实现类向量和类列表对象"，year = 2017, doi = "10.18129/B9.bioc. "S4Vectors”),sessioninfo =引文(“sessioninfo”),testthat =引文(“testthat ") ) ## ----' createData '------------------------------------------------------------- ## 创建一些玩具数据suppressPackageStartupMessages(图书馆(“IRanges”))set.seed (20140923) toyData < DataFrame(“sample1”= Rle(样本(0:10,1000年,真的),“sample2”= Rle(样本(0:10,1000年,真的),“之上”= Rle(样本(0:10,1000年,真的),“sample4”= Rle(样本(0:10,1000年,真的),“sample5”= Rle(样本(0:15,1000年,真的)),"sample6" = Rle(sample(0:15, 1000, TRUE))， "sample7" = Rle(sample(0:15, 1000, TRUE))， "sample8" = Rle(sample(0:15, 1000, TRUE))， "sample9" = Rle(sample(0:20, 1000, TRUE))， "sample10" = Rle(sample(0:20, 1000, TRUE)))， "sample11" = Rle(sample(0:20, 1000, TRUE)))， "sample12" = Rle(sample(0:20, 1000, TRUE)))， "sample13" = Rle(sample(0:20, 1000, TRUE))， "sample14" = Rle(sample(0:100, 1000, TRUE))， "sample15" = Rle(sample(0:100, 1000, TRUE))， "sample16" = Rle(sample(0:100, 1000, TRUE)， "##假设我们有4个组group <- factor(rep(toupper(letters[1:4])， each = 4)) ##注意，有些组有更高的覆盖率，我们可以在模型sampleDepth <- sapply(toyData, sum) sampleDepth ## ----'createModels'----------------------------------------------------------- ##构建模型矩阵mod <- model。矩阵(~ sampleDepth +集团)mod0 < - model.matrix (~ sampleDepth) # #探索他们国防部mod0 # #——“calculateFstats '-------------------------------------------------------- 库函数< - fstat(“derfinderHelper”)。应用数据= toyData (mod = mod, mod0 = mod0 scalefac = 1) fstat # #——createVignette eval = FALSE ----------------------------------------------- # ## 创建小插图#库(rmarkdown) # system.time derfinderHelper(渲染”。Rmd"， "BiocStyle::html_document")) ## ##提取R代码#库("knitr") #针织("derfinderHelper。限制型心肌病”,纠结= TRUE) # #——reproducibility1回声= FALSE --------------------------------------------- ## 装饰图案是Sys.time生成日期 () ## ---- reproducibility2,回声= FALSE --------------------------------------------- ## 处理时间以秒totalTime < - diff (c(开始时间,Sys.time()))轮(totalTime位数= 3)# #——reproducibility3,回声= FALSE ------------------------------------------------------------------------------------- ## 会话信息图书馆(“sessioninfo”)选项(宽度= 120)session_info () ## ---- vignetteBiblio,结果=“黑名单”,呼应= FALSE,警告= FALSE,消息= FALSE --------------------------------- ## 打印书目PrintBibliography(围涎,.opts =列表(超链接=“to.doc”,风格=“html”))