| MPAgenomics-package | Multi-Patient Analysis of Genomic Markers |
| MPAgenomics-package, | Multi-Patient Analysis of Genomic Markers |
| addChipType | Add a new chip type to the existing aroma architecture |
| addData | Add a new data-set to the existing aroma architecture |
| callingObject | Create the list of parameters for callingProcess function |
| callingProcess | Calling aberrations in segmented copy-number signal. |
| CNAobjectToCGHcallObject | Convert CNAobject |
| cnSegCallingProcess | Segment a copy-number signal and call the found segments. |
| createArchitecture | Create aroma architecture and copy files |
| createEmptyArchitecture | Create aroma architecture |
| filterSeg | Filter segments |
| findPlateau | Find the best choice of segmentation parameter. |
| getCopyNumberSignal | Extract copy-number signal from aroma files |
| getFracBSignal | Extract allele B fraction signal from aroma files |
| getGenotypeCalls | Extract genotype calls from aroma files |
| getListOfFiles | Get the contents of a data folder |
| getSymFracBSignal | Extract symmetrized allele B fraction signal from aroma files |
| HDlarsbivariate | lars algorithm for bivariate signal |
| markerSelection | markers selection |
| MPAgenomics | Multi-Patient Analysis of Genomic Markers |
| segFracBSignal | segmentation function for the allele B fraction |
| segmentation | segmentation function |
| segmentationAroma | segmentation function |
| segmentationObject | Create the list of parameters for segmentation function |
| SignalNormalization | Normalization process |
| signalPreProcess | Normalization process |
| symmetrizeFracB | symmetrize an allele B fraction signal |
| variableSelection | SNPs selection |