ChipEffectFile {aroma.affymetrix} | R Documentation |
The ChipEffectFile class
Description
Package: aroma.affymetrix
Class ChipEffectFile
Object
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FullNameInterface
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GenericDataFile
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CacheKeyInterface
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FileCacheKeyInterface
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AromaMicroarrayDataFile
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AromaPlatformInterface
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AffymetrixFile
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AffymetrixCelFile
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ParametersInterface
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ParameterCelFile
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ChipEffectFile
Directly known subclasses:
CnChipEffectFile, ExonChipEffectFile, SnpChipEffectFile
public abstract static class ChipEffectFile
extends ParameterCelFile
This class represents estimates of chip effects in the probe-level models.
Usage
ChipEffectFile(..., probeModel=c("pm"))
Arguments
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Fields and Methods
Methods:
extractMatrix | - | |
extractTheta | - | |
findUnitsTodo | - | |
getAM | - | |
readUnits | - | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, 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, names, objectSize, print, save, asThis
Author(s)
Henrik Bengtsson
See Also
An object of this class is typically obtained through the
getChipEffectSet()
method for the ProbeLevelModel
class.
An object of this class is typically part of a ChipEffectSet
.