IDProbes                Interactive version of genomePlot
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
compareSegmentations    Function for comparing segmentation methods to
                        a known truth
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
findBreakPoints         Returns the start and end of segments.
fit.model               Fitting a heterogneous HMM to the log2 ratios
                        on a particular chromosome.
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
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
nudSegmentation         Assigns each segment of each sample to either
                        'normal', 'up', 'down', 'amplified', or
                        'deleted'
plotSegmentedGenome     Plots the genome
processCGH              Process data in an MAList
read.clonesinfo         Reading chromsome and positional information
                        about each clone.
readPositionalInfo      readPositionalInfo
removeByWeights         Remove clones based on a weights matrix
runBioHMM               This function implements the BioHMM
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
runPicard               Results of segmenting an MAList data object
                        using the Picard et al algorithm found in the
                        tilingArray library
simulateData            A function for simulating aCGH data and the
                        corresponding clone layout
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
zoomChromosome          Interactive plot of a single chromsome
zoomGenome              Interactive plot of the whole genome
