## Not run:
# data(IlluminaMethylation)
#
# heatmap(IllumBeta, scale="n",
# col=colorRampPalette(c("yellow","black","blue"),space="Lab")(128))
#
# # Fit Gaussian RPMM
# rpmm <- blcTree(IllumBeta, verbose=0)
# rpmm
#
# # Get weight matrix and show first few rows
# rpmmWeightMatrix <- blcTreeLeafMatrix(rpmm)
# rpmmWeightMatrix[1:3,]
#
# # Get class assignments and compare with tissue
# rpmmClass <- blcTreeLeafClasses(rpmm)
# table(rpmmClass,tissue)
#
# # Plot fit
# par(mfrow=c(2,2))
# plot(rpmm) ; title("Image of RPMM Profile")
# plotTree.blcTree(rpmm) ; title("Dendrogram with Labels")
# plotTree.blcTree(rpmm,
# labelFunction=function(u,digits) table(as.character(tissue[u$index])))
# title("Dendrogram with Tissue Counts")
#
# # Alternate initialization
# rpmm2 <- blcTree(IllumBeta, verbose=0,
# initFunctions=list(blcInitializeSplitEigen(),
# blcInitializeSplitFanny(nu=2.5)))
# rpmm2
#
# # Alternate split criterion
# rpmm3 <- blcTree(IllumBeta, verbose=0, maxlev=3,
# splitCriterion=blcSplitCriterionLevelWtdBIC)
# rpmm3
#
# rpmm4 <- blcTree(IllumBeta, verbose=0, maxlev=3,
# splitCriterion=blcSplitCriterionJustRecordEverything)
# rpmm4$rLL$splitInfo$llike1
# rpmm4$rLL$splitInfo$llike2
# ## End(Not run)
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