ChipEffectSet {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ChipEffectSet
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
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"))
... |
Arguments passed to AffymetrixCelSet . |
probeModel |
The specific type of model, e.g. "pm" . |
Methods:
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, 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/)
An object of this class is typically obtained through the
getChipEffectSet()
method for the ProbeLevelModel
class.