AffymetrixCelSet: The AffymetrixCelSet class

Description

Package: aroma.affymetrix
Class AffymetrixCelSet

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

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

public static class AffymetrixCelSet
extends AffymetrixFileSet

An AffymetrixCelSet object represents a set of Affymetrix CEL files with identical chip types.

Usage

AffymetrixCelSet(files=NULL, ...)

Arguments

files: A list of AffymetrixCelFile:s.
...: Not used.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixCelSet`	-
	`byName`	-
	`doCRMAv1`	-
	`doCRMAv2`	-
	`doFIRMA`	-
	`doGCRMA`	-
	`doRMA`	-
	`extractAffyBatch`	-
	`extractFeatureSet`	-
	`extractMatrix`	-
	`getAverage`	-
	`getAverageAsinh`	-
	`getAverageFile`	-
	`getAverageLog`	-
	`getCdf`	-
	`getChipType`	-
	`getData`	-
	`getIntensities`	-
	`getPlatform`	-
	`getTimestamps`	-
	`getUnitGroupCellMap`	-
	`getUnitIntensities`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`justSNPRMA`	-
	`plotDensity`	-
	`readUnits`	-
	`setCdf`	-
	`writeSgr`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

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

Author

Henrik Bengtsson

Examples

Run this code

if (FALSE) {
  for (zzz in 0) {

# Find any dataset
path <- NULL
if (is.null(path))
  break

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define a dataset object based on all CEL files in a directory
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ds <- AffymetrixCelSet$fromFiles(path)
print(ds)

# Keep at most three arrays for this example
ds <- ds[1:min(3,nbrOfArrays(ds))]
print(ds)

} # for (zzz in 0)
rm(zzz)

}