GEList-class            Genomic Events - class
LargeDataObject-class   Large Data Object - class
SegList-class           Segmentation States - class
Viterbi.five            A scaled Viterbi algorithm for allocating
                        clones to one of five underlying states.
Viterbi.four            A scaled Viterbi algorithm for allocating
                        clones to one of four underlying states.
Viterbi.three           A scaled Viterbi algorithm for allocating
                        clones to one of two underlying states.
Viterbi.two             A scaled Viterbi algorithm for allocating
                        clones to one of two underlying states.
[.SegList               Subset SegList Objects
cbind.SegList           Combine SegList Objects
chrominfo.Mb            Basic Chromosomal Information for UCSC Human
                        Genome Assembly July 2003 freeze
computeSD               Function to estimate experimental variability
                        of a sample
convert.output          Converts the output from the simulation to a
                        format which can be used by segmentation
                        schemes available within R
dim.RGList              Retrieve the Dimensions of an RGList, MAList or
                        SegList Object
dimnames.SegList        Retrieve the Dimension Names of an RGList,
                        MAList or SegList Object
filterClones            Filter clones from sample
find.param.five         Yields the output in a model with five
                        underlying states
find.param.four         Yields output when there are 4 underlying
                        states
find.param.one          Yields output when there is 1 underlying states
find.param.three        Yields output when there are 3 underlying
                        states
find.param.two          Yields output when there are 2 underlying
                        states
findAberrations         Function to determines focal aberrations
findAmplifications      Function to determine high level amplifications
findBreakPoints         ~~function to do ... ~~
findGenomicEvents       Finds the genomic events associated with each
                        of the array CGH samples
findOutliers            Function to identify outlier clones
findTranslocations      Funtion identifying the transitions
fit.model               Fitting a heterogneous HMM to the log2 ratios
                        on a particular chromosome.
fitBioHMM               This function implements the BioHMM
fractionAltered         Function to compute fraction of genome altered
                        for each sample
genomePlot              Plots the genome
heatmapGenome           clustering and heatmap
imputeMissingValues     Imputing log2 ratios
log2ratios              Extracting log2 ratios
mergeStates             Funtion to merge states based on their state
                        means
mod.chrominfo           Chromosomal information
non.zero.length.distr.non.tiled
                        Empirical distribution of segment lengths in
                        non-tiled regions with copy number gains or
                        losses
non.zero.length.distr.tiled
                        Empirical distribution of segment lengths in
                        tiled regions with copy number gains or losses
plotGainLoss            frequency plots and significance analysis
plotSegmentationStates
                        Plotting the estimated hmm states and log2
                        ratios for each sample.
plotSegmentationSummary
                        plotSegmentationSummary
plotSegmentedGenome     Plots the genome
processCGH              Process data in aCGH object
read.clonesinfo         Reading chromsome and positional information
                        about each clone.
removeByWeights         Remove clones based on a weights matrix
runDNAcopy              Results of segmenting an MAList data object
                        using the DNAcopy library
runGLAD                 Results of segmenting an aCGHList data object
                        using the GLAD library
runHomHMM               A function to fit unsupervised Hidden Markov
                        model
sim.structure           A function for simulating aCGH data and the
                        corresponding clone layout
summarizeClones         Extracting summary information for all clones
threshold               Function to indicate gain or loss for each
                        clone for each sample
zero.length.distr.non.tiled
                        Empirical distribution of segment lengths in
                        non-tiled regions with no copy number gains or
                        losses
zero.length.distr.tiled
                        Empirical distribution of segment lengths in
                        tiled regions with no copy number gains or
                        losses
