CnChipEffectSet: The CnChipEffectSet class

Description

Package: aroma.affymetrix Class CnChipEffectSet

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFileSet ~~~~~~~~~~~~| ~~~~~~~~~~~~+--AromaMicroarrayDataSet ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpChipEffectSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnChipEffectSet

Directly known subclasses:

public static class CnChipEffectSet extends CopyNumberDataSet

This class represents estimates of chip effects in the probe-level models.

Usage

CnChipEffectSet(..., combineAlleles="byFirstFile")

Arguments

...

Arguments passed to SnpChipEffectSet.

combineAlleles

A logical indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

Methods:

	`as.CopyNumberDataSetTuple`
-
`exportTotalAndFracB`	-
	`extractTheta`
-
`extractTotalAndFreqB`	-
	`getAverageFile`
-
`getCombineAlleles`	-
	`hasAlleleBFractions`
-
`hasStrandiness`	-
	`setCombineAlleles`
-
`writeWig`	-

Methods inherited from CopyNumberDataSet: as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness Methods inherited from SnpChipEffectSet: byPath, exportTotalAndFracB, extractAlleleSet, extractCNT, extractSnpCnvQSet, extractSnpQSet, extractTheta, extractTotalAndFreqB, getAverageFile, getBaseline, getMergeStrands, setMergeStrands, writeCNT Methods inherited from ChipEffectSet: as.character, boxplotStats, byPath, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractAffyBatch, extractChromosomalDataFrame, extractExpressionSet, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getXAM, plotBoxplot, readUnits, updateUnits Methods inherited from ParameterCelSet: extractDataFrame, extractMatrix Methods inherited from ParametersInterface: getParameterSets, getParameters, getParametersAsString Methods inherited from AffymetrixCelSet: append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr Methods inherited from AffymetrixFileSet: as, as.AffymetrixFileSet, byPath, getDefaultFullName Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith Methods inherited from AromaMicroarrayDataSet: as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate Methods inherited from GenericDataFileSet: [, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApply, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName 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, objectSize, print, save, asThis