# # # R代码从装饰图案来源的小插曲SPIA /本月/ doc / SPIA。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:SPIA。Rnw: 75 - 79 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(SPIA)数据(colorectalcancer)选项(数字= 3)头(上)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:SPIA。Rnw: 99 - 108 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(hgu133plus2.db) x < - hgu133plus2ENTREZID顶级美元ENTREZ < -unlist (as.list (x ($ ID]))前<最高[! is.na(顶部ENTREZ美元),]前<最高[!复制(最高ENTREZ美元),]号<顶部(顶部adj.P.Val < 0.1,美元)DE_Colorectal =号$ logFC名称(DE_Colorectal) < -as.vector(一号ENTREZ美元)ALL_Colorectal =最高$ ENTREZ # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:SPIA。Rnw: 118 - 120 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # DE_Colorectal [1:10] ALL_Colorectal[1:10] # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:SPIA。Rnw: 127 - 133 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #通路分析基于证据;#使用nB = 2000或更多更准确的结果res = spia (de = DE_Colorectal = ALL_Colorectal,所有生物体=“保险”,nB = 2000,情节= FALSE,β= NULL,结合=“雪”,verbose = FALSE) #使输出符合这个屏幕res $ Name = substr (res名字美元1 10)#显示前15通路,省略KEGG链接res[1:20, -12] # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:spia。Rnw: 156 - 159 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotP (res,阈值= 0.05)点(我(日志(pPERT)) ~我(日志(pNDE)), data = res (res $ ID = = " 05210 "],坳=“绿色”,pch = 19日cex = 1.5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:SPIA。Rnw: 186 - 193 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # res $ pG = combfunc (res pNDE美元,res pPERT美元,结合=“norminv”) res $ pGFdr = p.adjust (res pG美元,“罗斯福”)res $ pGFWER = p.adjust (res pG美元,“bonferroni”) plotP (res,阈值= 0.05)点(我(日志(pPERT)) ~我(日志(pNDE)), data = res (res $ ID = = " 05210 "],坳=“绿色”,pch = 19日cex = 1.5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:SPIA。Rnw: 209 - 216 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(血管)#通路分析基础上结合证据;#使用nB = 2000或更多更准确的结果res < -spia (de = DE_Vessels = ALL_Vessels,所有生物体=“保险”,nB = 500,情节= FALSE,β= NULL, verbose = FALSE) #使输出符合这个屏幕res $ Name = substr (res名字美元1 10)#显示前15通路,省略KEGG链接res(1:15 -12) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:SPIA。Rnw: 222 - 223 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # res (“KEGGLINK”][20] # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:SPIA。Rnw: 235 - 246 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # rel < - c(“激活”、“复合”,“绑定/协会”、“表达”,“抑制”,“activation_phosphorylation”、“磷酸化”,“inhibition_phosphorylation”,“inhibition_dephosphorylation”、“分离”,“脱磷酸作用”,“activation_dephosphorylation”、“状态改变”,“activation_indirect效应”,“inhibition_ubiquination”、“ubiquination”、“expression_indirect效应”,“inhibition_indirect效应”、“压抑”、“dissociation_phosphorylation”、“间接effect_phosphorylation”、“activation_binding /协会”、“间接效应”,“activation_compound”、“activation_ubiquination”)β= c(1, 0, 0, 1, 1, - 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, - 1, 0, 0, 1, 0, 1, 1)名称(β)< rel cbind(β)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:SPIA。Rnw: 255 - 258 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #负载(文件=粘贴(执行(“extdata / hsaSPIA.RData”、包= " SPIA ")))的名字(path.info [[05210]]) path.info[[05210]][["激活"]](25:35,30:40)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:SPIA。Rnw: 267 - 286 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(图)库(Rgraphviz) plotG <函数(B) {nnms <零;书<零mynodes < -colnames (B) L <附些();n <暗(B)[1](我在1:n) {L[我]<附些(边缘= rownames (B) (abs (B[我])> 0])如果(和(B[我]! = 0)> 0){nnms < - c (nnms,粘贴(colnames (B)[我],rownames (B) (B[我]! = 0),9 = " ~ "))}}(L) < -rownames名字(B) g < - (“graphNEL”,节点= mynodes edgeL = L, edgemode =“指示”)情节(g)} # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:SPIA。Rnw: 295 - 296 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotG (path.info[[04012]][["激活"]])# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:SPIA。Rnw: 312 - 317 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # mydir =执行(“extdata / keggxml hsa”,包=“SPIA”) dir (mydir) makeSPIAdata (kgml.path = mydir有机体=“保险”,out.path = " . / ") res < -spia (de = DE_Colorectal = ALL_Colorectal,所有生物体=“保险”,data.dir = " . / ") res (-12)