# # # R '但代码从装饰图案来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:设置# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(“Biobase”)库(“注释”)库(GOstats)库(xtable)库(“相乘”)库(Rgraphviz)库(hgu95av2.db)库(GO.db)库(genefilter)库(“所有”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:例# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #的子集感兴趣:37 + 42个样本数据(所有)eset < -所有[,相交(grep (B“^”, as.character (BT)美元),这(as.character(所有摩尔美元)% % c (“BCR / ABL”、“否定”、“ALL1 / AF4”)))) MB =因素(eset mol.bio美元)至少7 # #强度高于100的样品f1 < - kOverA (7, log2 (100)) f2 =函数(x) {gps =分裂(2 ^ x, MB);mns =酸式焦磷酸钠(gps,意味着);如果(max (mns) - min (mns) < 100)假还真}ff < - filterfun (f1、f2)选择< - genefilter (eset ff)和(选择)esetSub <——eset(选中)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:mtFstats # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pvCutOff = 0.05 fstat = mt.maxT (exprs (esetSub) as.numeric (MB) 1, B = 1000,测试=“f”) eset = esetSub [fstat指数[fstat adjp美元 0 & & ! is.na (x [1])) = [hasBP] gg英镑英镑= lapp (igenes hasBP, makeGOGraph,“英国石油公司”,芯片=“hgu95av2.db”) # #也可以做ggx = lapp(英镑、GOGraph GOBPPARENTS) # #和simatM1 =应该得到相同的矩阵(1、nr = (hasBP)和数控=总和(hasBP)),(我在1:sum (hasBP))为(1 j: sum (hasBP))如果其他(i = = j)下simatM1 (i, j) = simUI (gg[[我]],gg [[j]])图书馆(“RBGL”) simatM2 =矩阵(1、nr = (hasBP)和数控=总和(hasBP)),(我在1:sum (hasBP))为(1 j: sum (hasBP))如果其他(i = = j)下{simatM2 (i, j) = simLP (gg[[我]],gg [[j]])} # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号: