Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectSet
Directly known subclasses:
CnChipEffectSet, ExonChipEffectSet, SnpChipEffectSet
public static class ChipEffectSet
extends ParameterCelSet
This class represents estimates of chip effects in the probe-level models.ChipEffectSet(..., probeModel=c("pm"))AffymetrixCelSet."pm".boxplotStats -
calculateBaseline Estimates the baseline signal chromosome by chromosome.
calculateFieldBoxplotStats -
calculateNuseBoxplotStats -
calculateRleBoxplotStats -
extractChromosomalDataFrame -
extractMatrix -
extractTheta -
findByName -
findUnitsTodo -
fromDataSet -
getAM Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file.
getAverageFile -
getBaseline Gets the baseline signals across chromosomes.
getCellIndices -
getParameters -
getXAM Gets the physical position, log-intensities and log-ratios of chip effects for two arrays.
plotBoxplot -
readUnits -
}
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from AffymetrixCelSet:
[, [[, append, as, as.AffymetrixCelSet, averageQuantile, byName, byPath, convertToUnique, doCRMAv1, doCRMAv2, extractAffyBatch, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAverageFile, getChipType, getDefaultFullName, getPlatform, nbrOfArrays, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
getParentName, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, appendFullNamesTranslatorByNULL, as.list, byName, byPath, clearCache, clearFullNamesTranslator, copyTo, equals, extract, findByName, getAlias, getDefaultFullName, getFile, getFileClass, getFileSize, getFullNames, getNames, getPath, getPathnames, hasFile, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullNamesTranslator, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, savegetChipEffectSet() method for the ProbeLevelModel class.