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| SIM-package | Statistical Integration of Microarrays |
| acgh.data | Array-comparative genomic hybridization data example |
| assemble.data | Assemble the data to run the integrated analysis |
| chrom.table | Table with chromosome arm positions |
| expr.data | Expression data example |
| impute.nas.by.surrounding | Impute NA's in array-CGH data |
| integrated.analysis | Integrated analysis of expression and copy number 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 | Statistical Integration of Microarrays |
| 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.zscore.heatmap | Association heatmap from z-scores |
| 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 |