Package: aroma.core
Class CopyNumberChromosomalModel
Object
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ChromosomalModel
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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, ...)
A CopyNumberDataSetTuple
.
An optional CopyNumberDataFile
,
or CopyNumberDataSet
or CopyNumberDataSetTuple
for pairwise comparisons.
A logical
specifying whether ratios should
be calculated relative to the reference.
If FALSE
, argument refTuple
is ignored.
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.
Henrik Bengtsson