acgh.data               Array Comparative Genomic Hybridization data
assemble.data           Assemble the data to run the integrated
                        analysis
chrom.table             Table with chromosome information
expr.data               Expression data example
getoverlappingregions   Get the overlapping regions between independent
                        and dependent regions
impute.nas.by.surrounding
                        Impute NA's in array-CGH data
integrated.analysis     Integrated analysis of dependent and indepedent
                        microarray data
link.metadata           Link a metadata annotation file to expression
                        ID
RESOURCERER.annotation.to.ID
                        Link RESOURCERER annotation file to expression
                        ID
samples                 Samples for example data
SIM-package             Statistical Integration of Microarrays
sim.plot.overlapping.indep.dep.features
                        P-value plot and mean-zscore plots with
                        indication of overlapping features.
sim.plot.pvals.on.genome
                        Plot the P-values in whole genome overview
sim.plot.pvals.on.region
                        P-value histograms and P-values along the
                        genome per region
sim.plot.zoom.in        Zoom in on heatmap
sim.plot.zscore.heatmap
                        Association heatmap from z-scores
sim.update.chrom.table
                        Update the chromomosome table
tabulate.pvals          Sums significant P-values for the analyzed
                        regions
tabulate.top.dep.features
                        Lists the P-values for the dependent features
tabulate.top.indep.features
                        Lists the mean z-scores for the independent
                        features
