aroma.affymetrix (version 2.2.0)

AffymetrixFile: The abstract AffymetrixFile class

Description

Package: aroma.affymetrix Class AffymetrixFile Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--AromaMicroarrayDataFile ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile Directly known subclasses: AffymetrixCdfFile, AffymetrixCelFile, AffymetrixCnChpFile, AffymetrixTsvFile, AromaChipTypeAnnotationFile, ChipEffectFile, CnagCfhFile, CnChipEffectFile, CnProbeAffinityFile, DChipCdfBinFile, DChipDcpFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile public abstract static class AffymetrixFile extends AromaPlatformInterface An AffymetrixFile object represents a single Affymetrix file, e.g. an Affymetrix CEL file or an Affymetrix CDF file. Note that this class is abstract and can not be instanciated, but instead you have to use one of the subclasses or the generic fromFile() method.

Usage

AffymetrixFile(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods: No methods defined. 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 part of an AffymetrixFileSet.