# # # R代码从装饰图案的火神源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:火神。Rnw: 65 - 66 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # set.seed(1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:火神。Rnw: 69 - 73 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #如果!requireNamespace (“BiocManager”,悄悄地= TRUE)) # # install.packages (“BiocManager”) # # BiocManager::安装(“vulcandata”) # # BiocManager::安装(“火神”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 3号代码块:火神。Rnw: 79 - 80 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(火神)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:火神。Rnw: 84 - 85 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(vulcandata) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:火神。Rnw: 92 - 95 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #从虚拟ChIP-Seq数据集生成一个注释文件vfile < -tempfile () vulcandata:: vulcansheet (vfile) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:火神。Rnw: 99 - 103 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BAM和床信息导入列表对象vobj < -vulcan.import (vfile) vobj < -vulcandata: vulcanexample()拆开(vfile) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:火神。Rnw: 107 - 109 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #注释山峰基因名称vobj < -vulcan.annotate (vobj lborder = -10000, rborder = 10000,方法=“总和”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:火神。Rnw: 113 - 117 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #火神规范化数据分析vobj < -vulcan.normalize (vobj) #检测条件存在在我们的进口对象名称(vobj样本美元)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:火神。Rnw: 123 - 124 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #负载(执行(“extdata”、“network.rda”、包=“vulcandata mustWork = TRUE)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:火神。Rnw: 133 - 135 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # vobj_analysis <火神(vobj、网络=网络,对比= c (“t90”、“t0”), minsize = 5)情节(vobj_analysis msviper美元,夫人= 7)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:火神。Rnw: 148 - 152 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # reflist < -setNames(传言称(rnorm (1000)), paste0(“基因”,1:1000))设置< -paste0(“基因”,示例(1∶50)obj < gsea (reflist、设置方法=“帕累托”)obj $ p。值# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:火神。Rnw: 155 - 156 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plot_gsea (obj) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:火神。Rnw:163-169 ################################################### signatures<-setNames(-sort(rnorm(1000)),paste0("gene",1:1000)) set1<-paste0("gene",sample(1:200,50)) set2<-paste0("gene",sample(1:1000,50)) groups<-list(set1=set1,set2=set2) obj<-rea(signatures=signatures,groups=groups) obj ################################################### ### code chunk number 14: vulcan.Rnw:177-191 ################################################### par(mfrow=c(1,2)) # Thousands set.seed(1) a<-runif(1000,0,1e4) plot(a,yaxt="n") kmg<-kmgformat(pretty(a)) axis(2,at=pretty(a),labels=kmg) # Millions to Billions set.seed(1) a<-runif(1000,0,1e9) plot(a,yaxt="n",pch=20,col=val2col(a)) kmg<-kmgformat(pretty(a)) axis(2,at=pretty(a),labels=kmg)