## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----setup, include=FALSE-------------------------------------------------- library(knitr) ## ----results='hide',message=FALSE------------------------------------------ library(mAPKL) library(mAPKLData) data(mAPKLData) varLabels(mAPKLData) breast <- sampling(Data=mAPKLData, valPercent=40, classLabels="type", seed=135) ## ----tidy=TRUE------------------------------------------------------------- breast ## ----tidy=TRUE,results='hide',message=FALSE-------------------------------- normTrainData <- preprocess(breast$trainData) normTestData <- preprocess(breast$testData) ## ----tidy=TRUE------------------------------------------------------------- attributes(normTrainData) ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60)----------------------------- exprs(breast$trainData)<-normTrainData$clL2.normdata exprs(breast$testData)<-normTestData$clL2.normdata out.clL2 <- mAPKL(trObj=breast$trainData, classLabels="type", valObj=breast$testData,dataType=7) ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60)----------------------------- clasPred <- classification(out.clL2@exemplTrain,"type",out.clL2@exemplTest) ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60),message=FALSE--------------- gene.info <- annotate(out.clL2@exemplars,"hgu133plus2.db") gene.info@results ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60),message=FALSE--------------- probes2pathways(gene.info) ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60),message=FALSE--------------- net.attr <- netwAttr(out.clL2) wDegreeL <- net.attr@degree$WdegreeL[out.clL2@exemplars] wClosenessL <- net.attr@closeness$WclosenessL[out.clL2@exemplars] wBetweenessL <- net.attr@betweenness$WbetweennessL[out.clL2@exemplars] wTransitivityL <- net.attr@transitivity$WtransitivityL[out.clL2@exemplars] ## ----tidy=TRUE,tidy.opts=list(width.cutoff=60)----------------------------- Global.val <- c(net.attr@degree$WdegreeG, net.attr@closeness$WclosenessG, net.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()