## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----loading, fig.width=6, fig.height=6, echo=TRUE------------------------- library(Pigengene) data(aml) data(mds) d1 <- rbind(aml,mds) Labels <- c(rep("AML",nrow(aml)),rep("MDS",nrow(mds))) names(Labels) <- rownames(d1) Disease <- as.data.frame(Labels) h1 <- pheatmap.type(d1[,1:20],annRow=Disease,show_rownames=FALSE) ## ----oneStep, echo=TRUE---------------------------------------------------- p1 <- one.step.pigengene(Data=d1,saveDir='pigengene', bnNum=0, verbose=1, seed=1, Labels=Labels, toCompact=FALSE, doHeat=FALSE) ## ----tree, fig.width=5, fig.height=5, echo=TRUE---------------------------- plot(p1$c5treeRes$c5Trees[["34"]]) ## ----pigengene, fig.width=5, fig.height=5, echo=TRUE----------------------- dim(p1$pigengene$eigengenes) p1 <- pheatmap.type(p1$pigengene$eigengenes,annRow=Disease,show_rownames=FALSE) ## ----citation, results='asis', eval=TRUE----------------------------------- citation("Pigengene") ## ----sessionInfo, results='asis', eval=TRUE-------------------------------- toLatex(sessionInfo())