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

AffymetrixFileSet

R Documentation

The AffymetrixFileSet class

Description

Package: aroma.affymetrix
Class AffymetrixFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet

Directly known subclasses:
AffymetrixCelSet, AffymetrixCnChpSet, ChipEffectSet, CnChipEffectSet, DChipDcpSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet

public abstract static class AffymetrixFileSet
extends AromaPlatformInterface

An AffymetrixFileSet object represents a set of AffymetrixFiles with identical chip types.

Usage

AffymetrixFileSet(files=NULL, ...)

Arguments

`files`	A `list` of `AffymetrixFile`:s.
`...`	Arguments passed to `GenericDataFileSet`.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixFileSet`	-
	`byPath`	-

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, 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