aroma.affymetrix (version 2.2.0)

ChipEffectFile: The ChipEffectFile class

Description

Package: aroma.affymetrix Class ChipEffectFile Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--AromaMicroarrayDataFile ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--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 ParameterCelFile.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods: rll{ extractChromosomalDataFrame - extractMatrix - extractTheta - findUnitsTodo - getAM Gets the log-intensities and log-ratios of chip effects for two arrays. getCellIndices - getCellMapForMainCdf - getExpandedCellMap - getParameters - getUnitGroupCellChromosomePositionMap - getXAM Gets the physical position, log-intensities and log-ratios of chip effects for two arrays. readUnits - } Methods inherited from ParameterCelFile: extractDataFrame, extractMatrix, getParameters, readUnits Methods inherited from AffymetrixCelFile: [, [[, allocateFromCdf, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, setCdf, smoothScatterMvsA, writeImage Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith Methods inherited from AromaMicroarrayDataFile: getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributesByTags, setAttributeXY Methods inherited from GenericDataFile: getParentName, compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName Methods inherited from Object: asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

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.