# #——style-knitr eval = TRUE,呼应= FALSE,结果= "飞机 "-------------------- BiocStyle:乳胶 () ## ---- 设置,包括= FALSE -------------------------------------------------- 库(knitr) # # =“隐藏”——结果,消息= FALSE ------------------------------------------ 图书馆(mAPKL)图书馆(mAPKLData)数据(mAPKLData) varLabels (mAPKLData)乳房< -抽样(data = mAPKLData valPercent = 40 classLabels =“类型”,种子= 135)# #——整洁= TRUE ------------------------------------------------------------- 乳房# #——整洁= TRUE,结果=“隐藏”,消息= FALSE -------------------------------- normTrainData < -预处理(乳房trainData美元)normTestData < -预处理(乳房testData美元)# #——整洁= TRUE ------------------------------------------------------------- 属性(normTrainData) # #——整洁= TRUE, tidy.opts =列表(width.cutoff = 60 )----------------------------- exprs(乳房trainData美元)< -normTrainData clL2美元。normdata exprs(乳房testData美元)< -normTestData clL2美元。normdata出来。clL2 <- mAPKL(trObj=breast$trainData, classLabels="type"，valObj =乳房testData美元,数据类型= 7)# #——整洁= TRUE, tidy.opts =列表(width.cutoff = 60 )----------------------------- clasPred < -分类(“类型”,out.clL2@exemplTrain out.clL2@exemplTest) # #——整洁= TRUE, tidy.opts =列表(width.cutoff = 60),消息= FALSE --------------- gene.info < -注释(out.clL2@exemplars hgu133plus2.db) gene.info@results # #——整洁= TRUE, tidy.opts =列表(width.cutoff = 60),消息= FALSE --------------- probes2pathways (gene.info) # #——整理= TRUE, tidy.opts =列表(width.cutoff = 60),消息= FALSE --------------- 网。attr <- netwAttr(out. cll2) wDegreeL <- net.attr@degree$ wDegreeL [out. cll2]。clL2@exemplars] wClosenessL <- net.attr@closeness$ wClosenessL [out.]clL2@exemplars] wBetweenessL <- net.attr@betweenness$ wBetweenessL [out.]clL2@exemplars] wTransitivityL <- net.attr@transitivity$ wTransitivityL [out.]clL2@exemplars) # #——整洁= TRUE, tidy.opts =列表(width.cutoff = 60 )----------------------------- 全球。val < - c(净。attr@degree WdegreeG美元,净。attr@closeness WclosenessG美元,净。attr@betweenness$WbetweennessG, net.attr@transitivity$WtransitivityG) ## ----tidy=TRUE------------------------------------------------------------- Global.val <- round(Global.val,2) exempl.netattr <- rbind(wDegreeL,wClosenessL,wBetweenessL,wTransitivityL) ## ----tidy=TRUE------------------------------------------------------------- netAttr <- cbind(Global.val,exempl.netattr) netAttr <- t(netAttr) netAttr ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60),message=FALSE--------------- # For local degree > global + standard deviation sdev<-sd(net.attr@degree$WdegreeL) msd <- net.attr@degree$WdegreeG + sdev hubs <- wDegreeL[which(wDegreeL > msd)] hubs ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60),message=FALSE--------------- sdev<-sd(net.attr@degree$WdegreeL) ms2d <- net.attr@degree$WdegreeG + 2*sdev net <- net.attr@degree$WdegreeL[which(net.attr@degree$WdegreeL > ms2d)] idx <- which(net.attr@edgelist[,1] %in% names(net)) new.edgeList <- net.attr@edgelist[idx,] dim(new.edgeList) require(igraph) g=graph.data.frame(new.edgeList,directed=FALSE) #tkplot(g,layout=layout.fruchterman.reingold) ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60)----------------------------- sessionInfo()