| Function | Description |
| arrayTrend | Spatial trend of microarray spots statistic |
| clone.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| detectSB | Spatial bias detection |
| flag | Create an object of type flag |
| flag.arrayCGH | Apply a flag to an arrayCGH |
| flags | Examples of flag objects to apply to CGH arrays |
| flag.summary | Summarize information about flags after array normalization |
| genome.plot | Display a pan-genomic representation of a normalized arrayCGH |
| html.report | Generate an HTML report of array normalization |
| import | Import raw file to an arrayCGH object |
| nem | Spatial Classification by EM algorithm |
| norm.arrayCGH | Normalize an object of type arrayCGH |
| qscore | Create an object of type qscore |
| qscore.arrayCGH | Compute a quality score for a given arrayCGH |
| qscore.summary | Compute quality scores for a given arrayCGH object |
| report.plot | Display an array image and a genomic representation of a normalized arrayCGH |
| sort.arrayCGH | sort clone-level information of a normalizaed arrayCGH object |
| spatial | Examples of array-CGH data with spatial artifacts |