# # # R代码从装饰图案来源的小插曲PGSEA /本月/ doc / PGSEA。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:PGSEA。Rnw: 40-43 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(PGSEA)基本< - - - - - -新(smc、id = c(“基因”,“b基因”),参考=“简单smc”) str(基本)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:PGSEA。Rnw: 50-53 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # datadir < -系统。文件(“extdata”,包=“PGSEA”) < - readGmt(文件示例。路径(datadir sample.gmt)) str(样本[1])# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:PGSEA。Rnw: 58 - 61 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(nbEset) pg <——PGSEA (nbEset cl =样本,ref = 1:5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:PGSEA。Rnw: 66 - 69 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #子< -因子(c(代表(NA, 5),代表(“NeuroB”, 5),代表(“NeuroB_MYC + 5))) smcPlot (pg(,)、子、规模= c(-12年,12),show.grid = T)利润= c(1、7、13)坳= .rwb) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:PGSEA。Rnw: 77 - 80 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # mcs < - go2smc () [1:10] pg <——PGSEA (nbEset, cl = mcs, ref = 1:5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:PGSEA。Rnw: 85 - 88 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # smcPlot (pg(,)、子、规模= c(-12年,12),show.grid = T)利润= c(20) 1 1 7日,卡扎菲= .rwb) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:PGSEA。Rnw: 98 - 102 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (VAImcs)数据(VAIgsc) pg <——PGSEA (nbEset, cl = VAIgsc ref = 1:5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:PGSEA。Rnw: 107 - 110 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # smcPlot (pg(,)、子、规模= c (5,5), show.grid = T)利润= c(1、1、8、14),坳= .rwb r.cex = 7)