CnChipEffectSet {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class CnChipEffectSet
Object
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GenericDataFileSet
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AromaMicroarrayDataSet
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AromaPlatformInterface
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AffymetrixFileSet
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AffymetrixCelSet
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ParameterCelSet
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ChipEffectSet
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SnpChipEffectSet
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CnChipEffectSet
Directly known subclasses:
public static class CnChipEffectSet
extends SnpChipEffectSet
This class represents estimates of chip effects in the probe-level models.
CnChipEffectSet(..., combineAlleles="byFirstFile")
... |
Arguments passed to SnpChipEffectSet . |
combineAlleles |
A logical indicating if the signals from
allele A and allele B are combined or not. |
Methods:
exportTotalAndFracB | - | |
extractTheta | - | |
extractTotalAndFreqB | - | |
getAverageFile | - | |
getBaseline | - | |
getCombineAlleles | - | |
setCombineAlleles | - | |
writeWig | - |
Methods inherited from SnpChipEffectSet:
exportTotalAndFracB, extractCNT, extractSnpCnvQSet, extractSnpQSet, extractTheta, extractTotalAndFreqB, fromFiles, getAverageFile, getBaseline, getMergeStrands, setMergeStrands, writeCNT
Methods inherited from ChipEffectSet:
boxplotStats, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractChromosomalDataFrame, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, fromFiles, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getParameters, getXAM, plotBoxplot, readUnits, updateUnits
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from AffymetrixCelSet:
[, [[, append, as, as.AffymetrixCelSet, averageQuantile, byName, convertToUnique, extractAffyBatch, extractMatrix, findByName, fromFiles, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getFullName, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, fromFiles
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile
Methods inherited from AromaMicroarrayDataSet:
getChipType, getPlatform, nbrOfArrays, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
append, appendFiles, as.list, byName, clearCache, copyTo, equals, extract, findByName, fromFiles, getAlias, getFile, getFileClass, getFileSize, getFullName, getFullNames, getFullNameTranslator, getName, getNames, getPath, getPathnames, getTags, hasFile, hasTag, hasTags, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullName, setFullNamesTranslator, setFullNameTranslator, setName, setTags, update2, validate
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, save
Henrik Bengtsson (http://www.braju.com/R/)