ChromosomeModels-class
                        Class "ChromosomeModels"
GeneDependencyModel-class
                        Class "GeneDependencyModel"
GenomeModels-class      Class "GenomeModels"
fit.byname              Fit dependency model around one gene 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
get.neighboring.probes
                        Get neighboring probes
get.neighs              get.neighs
join.top.regions        Merge the overlapping top chromosomal regions.
order.feature.info      Order the gene information table by chromosomal
                        locations.
pint.data               Forms a data set and pairs samples in two data
                        sets.
plot.GeneDependencyModel
                        Dependency score plotting
screen.cgh.mrna         Fits dependency models to chromosomal arm,
                        chromosome or the whole genome.
summarize.region.parameters
                        Summarize overlapping models.
z.effects               The model parameters z and W
