Package: aroma.core Class CopyNumberChromosomalModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
Directly known subclasses: CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel
public abstract static class CopyNumberChromosomalModel extends ChromosomalModel
This abstract class represents a copy-number model.
CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*",
genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)
An optional CopyNumberDataFile
,
or CopyNumberDataSet
or CopyNumberDataSetTuple
for pairwise comparisons.
A character
string specifying what genome is process.
(optional) A vector
specifying which chromosomes
to process.
A double
in [0,1] indicating how many non-finite
signals are allowed in the sanity checks of the data.
Optional arguments that may be used by some of the subclass models.
Methods:
extractRawCopyNumbers |
Extracts relative copy numbers. | |
fit |
Fits the model. | |
getChromosomeLength |
- | |
getNames |
- | |
getReference |
- | |
isPaired |
- |
Methods inherited from ChromosomalModel: as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome
Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires genome information annotation files for every chip type.