AffymetrixFile: The abstract AffymetrixFile class

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

The abstract AffymetrixFile class

Description

Package: aroma.affymetrix
Class AffymetrixFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile

Directly known subclasses:
AffymetrixCdfFile, AffymetrixCelFile, AffymetrixCnChpFile, AffymetrixPgfFile, AffymetrixTsvFile, AromaChipTypeAnnotationFile, ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, CnagCfhFile, 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, 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 part of an AffymetrixFileSet.

aroma.affymetrix documentation built on May 29, 2024, 4:32 a.m.