# # # R代码从装饰图案来源的小插曲PADOG /本月/ doc / PADOG。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1:图一# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(KEGGdzPathwaysGEO)库(PADOG) set.seed (1) =“GSE9348”数据集(=组列表,包=“KEGGdzPathwaysGEO”) x =得到数据集(套)#提取所需信息exp = experimentData (x);数据集= exp@name dat.m = exprs (x)去年= pData (x)设计=笔记(exp)美元设计注释=粘贴(x@annotation,“.db”, 9 = " ") targetGeneSets =笔记(exp)美元targetGeneSets # KEGG通路上运行padog函数#使用准确的结果最高产量研究= padog倪= 1000 (esetm = dat。m组=美元另组、配对设计= = =“配对”,块=另块美元,targetgs = targetGeneSets gslist = " KEGG注释=注释。db”,生物= " hsa " verbose = FALSE, Nmin = 3,倪= 50,情节= TRUE)最高产量研究(1:15,- c(4、5)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:PADOG。Rnw: 169 - 225 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # randomF = function(集、mygslist minsize) {set.seed(1) #这加载数据集在一个名为x的ExpressionSet对象数据(=组列表,包=“KEGGdzPathwaysGEO”) x =得到数据集(套)#提取所需的信息传递给padog exp = experimentData (x);dat.m = exprs (x)去年= pData数据集(x) = exp@name设计=笔记(exp)设计注释美元=粘贴(x@annotation,“.db”, 9 = " ") targetGeneSets =笔记(exp) targetGeneSets #摆脱重复probesets美元ENTREZ ID通过保持probeset #与最小的假定值(计算使用limma) aT1 = filteranot (esetm = dat.m组=美元另组、配对=(设计= =“配对”),块=另块美元,注释=注释)#创建一个输出dataframe这个玩具方法和随机基因集假定值mygslistSize = unlist(拉普兰人(mygslist,函数(x){长度(相交(aT1 ENTREZID美元,x))})) res = data.frame (ID =名字(mygslist), P = runif(长度(mygslist)),大小= mygslistSize stringsAsFactors = FALSE) res $罗斯福= p.adjust (res $ P,“罗斯福”)#下降genesets不到minsize基因在当前数据集res = res (res大小> = minsize美元)#美元计算排名res等级=等级(res $ P) /暗(res)[1] * 100 #需要比较方法之间的排名;必须一样鉴于mymethods #参数”名单(myRand = myRand“res $方法=;#需要因为等级配对方法之间的比较数据集水平res美元数据集<数据集;targetGeneSets # #只输出结果集将相关基因的这个数据集返回(res (res $ ID % % targetGeneSets))} #所有24个数据集上运行分析和比较新的方法与# PADOG和GSA myRand(如果安装)(选为参考上市以来第一次在existingMethods) #如果包平行安装并行数据集进行分析。# = compPADOG(数据集= NULL, existingMethods = c (“GSA”、“PADOG”), # mymethods =列表(myRand = randomF), # gslist =“KEGG.db”, Nmin = 3,倪= 1000,情节= TRUE, verbose = FALSE) #比较myRand对PADOG 4只数据集# mysets =数据(包=“KEGGdzPathwaysGEO”)结果(“项目”)美元mysets = c (“GSE9348”、“GSE8671”,“GSE1297”)出= compPADOG(数据集= mysets existingMethods = c (“PADOG”), mymethods = (myRand = randomF)列表,gslist =“KEGG.db”, Nmin = 3,倪= 40块= TRUE, verbose = FALSE)打印(出)