blcTree: Beta RPMM Tree

Description

Performs beta latent class modeling using recursively-partitioned mixture model

Usage

blcTree(x, initFunctions = list(blcInitializeSplitFanny()),  weight = NULL, index = NULL, wthresh = 1e-08, nodename = "root", maxlevel = Inf, verbose = 2, nthresh = 5, level = 0, env = NULL,  unsplit = NULL, splitCriterion = blcSplitCriterionBIC)

Arguments

Data matrix (n x j) on which to perform clustering. Missing values are supported. All values should lie strictly between 0 and 1.

initFunctions

List of functions of type “blcInitialize...” for initializing latent class model. See blcInitializeFanny for an example of arguments and return values.

weight

Weight corresponding to the indices passed (see index). Defaults to 1 for all indices

index

Row indices of data matrix to include. Defaults to all (1 to n).

wthresh

Weight threshold for filtering data to children. Indices having weight less than this value will not be passed to children nodes. Default=1E-8.

nodename

Name of object that will represent node in tree data object. Defaults to “root”. USER SHOULD NOT SET THIS.

maxlevel

Maximum depth to recurse. Default=Inf.

verbose

Level of verbosity. Default=2 (too much). 0 for quiet.

nthresh

Total weight in node required for node to be a candidate for splitting. Nodes with weight less than this value will never split. Defaults to 5.

level

Current level. Defaults to 0. USER SHUOLD NOT SET THIS.

env

Object of class “blcTree” to store tree data. Defaults to a new object. USER SHOULD NOT SET THIS.

unsplit

Latent class parameters from parent, to store in current node. Defaults to NULL for root. This is used in plotting functions. USER SHOULD NOT SET THIS.

splitCriterion

Function of type “blcSplitCriterion...” for determining whether a node should be split. See blcSplitCriterionBIC for an example of arguments and return values.

Value

An object of class “blcTree”. This is an environment, each of whose component objects represents a node in the tree.

Details

This function is called recursively by itself. Upon each recursion, certain arguments (e.g. nodename) are reset. Do not attempt to set these arguments yourself.

References

Houseman et al., Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 9:365, 2008.

Examples

Run this code

## 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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