ChromosomeArmModels-class
                        Class "ChromosomeArmModels", for dependency
                        models in chromosomal arm
ChromosomeModels-class
                        Class "ChromosomeModels"
DependencyModel-class   Class "DependencyModel"
GenomeModels-class      Class "GenomeModels"
fit.byname              Fit dependency model around one gene between
                        two data sets.
fit.dependency.model    Fit dependency model between two data sets.
fixed.window            Form data with a selected window size for the
                        model fitting
geneCopyNum             Gene copy number data in chromosome 17
geneExp                 Gene expression data in chromosome 17
pint.data               Forms a data set and pairs samples in two data
                        sets.
plot.DependencyModel    Dependency score plotting
screen.cgh.mrna         Fits dependency models to chromosomal arm,
                        chromosome or the whole genome.
z.expectation           The model parameters z and W
