# # # R代码从装饰图案的CGHcall来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:CGHcall。Rnw: 50-53 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(CGHcall)数据(萎蔫)萎蔫<——make_cghRaw(萎蔫)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:CGHcall。Rnw: 65 - 66 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # cghdata <——预处理(nchrom萎蔫,maxmiss = 30日= 22)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:CGHcall。Rnw: 75 - 77 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #常态。cghdata < -正常化(cghdata、方法=“中位数”,smoothOutliers = TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:CGHcall。Rnw: 89 - 92 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #常态。cghdata < -常态。cghdata[1:2]凹陷。cghdata < segmentData(常态。cghdata、方法= " DNAcopy " undo.splits =“sdundo”,撤销。SD = 3, clen = 10, relSDlong = 5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:CGHcall。Rnw: 97 - 98 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # postseg。cghdata < - postsegnormalize (seg.cghdata) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:CGHcall。Rnw: 106 - 108 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #肿瘤。道具< - c(0.75, 0.9)结果<——CGHcall (postseg.cghdata类= 5,多孔性= tumor.prop) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:CGHcall。Rnw:113-114 ################################################### result <- ExpandCGHcall(result,postseg.cghdata) ################################################### ### code chunk number 8: CGHcall.Rnw:122-123 ################################################### plot(result[,1]) ################################################### ### code chunk number 9: CGHcall.Rnw:129-130 ################################################### plot(result[,2]) ################################################### ### code chunk number 10: CGHcall.Rnw:139-140 ################################################### summaryPlot(result) ################################################### ### code chunk number 11: CGHcall.Rnw:149-150 ################################################### frequencyPlotCalls(result)