# # # R代码从装饰图案的ChIPComp来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶(use.unsrturl = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:ChIPComp。Rnw: 57 - 61 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(ChIPComp)相依= makeConf(系统。文件(“extdata”、“conf.csv”、包=“ChIPComp”))相依=参看参看设计=相依美元设计# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:ChIPComp。Rnw: 64 - 76 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #相依= data.frame (SampleID = 1:4,条件= c (“Helas3”、“Helas3”,“K562”、“K562”),因子= c (“H3k27ac”、“H3k27ac”,“H3k27ac”、“H3k27ac”), ipReads =执行(“extdata”, c (“Helas3.ip1.bed”、“Helas3.ip2.bed”,“K562.ip1.bed”、“K562.ip2.bed”),包=“ChIPComp”), ctReads =执行(“extdata”, c (“Helas3.ct.bed”、“Helas3.ct.bed”,“K562.ct.bed”、“K562.ct.bed”),包=“ChIPComp”),峰值=执行(“extdata”, c (“Helas3.peak.bed”、“Helas3.peak.bed”,“K562.peak.bed”、“K562.peak.bed”),包=“ChIPComp”))相依条件=美元因素(conf美元条件)conf美元因素=因素(conf美元因素)设计= as.data.frame(拉普兰人(参看[c(“条件”、“因素”)],as.numeric)) 1设计= as.data.frame (model.matrix(~条件,设计)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:ChIPComp。Rnw: 80 - 81 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # countSet = makeCountSet(配置、设计、文件类型=“床”,物种=“hg19 binsize = 1000) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:figureexample # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #地块(countSet) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:ChIPComp。Rnw: 91 - 93 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # countSet = ChIPComp (countSet)打印(countSet) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:ChIPComp。Rnw: 97 - 98 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(seqData) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:sessionInfo # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # toLatex (sessionInfo ())