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-package | 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 |
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