aroma.affymetrix (version 2.11.1)

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: rll{ as - as.AffymetrixCelSet Coerce an object to an AffymetrixCelSet object. byName - doCRMAv1 - doCRMAv2 - doFIRMA - doGCRMA - doRMA - extractAffyBatch Extracts an in-memory AffyBatch object from the CEL set. extractFeatureSet Extracts CEL signals an in-memory FeatureSet object. extractMatrix Extract data as a matrix for a set of arrays. getAverage - getAverageAsinh - getAverageFile Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set. getAverageLog - getCdf Gets the CDF structure for this CEL set. getChipType Gets the chip type for this CEL set. getData - getIntensities Gets cell intensities from a set of cells and a set of arrays. getPlatform - getTimestamps - getUnitGroupCellMap - getUnitIntensities Gets cell signals for a subset of units and a subset of arrays. getUnitNamesFile - getUnitTypesFile - justSNPRMA - plotDensity Plots the densities of all samples. readUnits - setCdf Sets the CDF structure for this CEL set. writeSgr - }

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

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

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

Methods inherited from GenericDataFileSet: [, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, equals, extract, findByName, getChecksum, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, hasFile, indexOf, nbrOfFiles, resetFullNames, seq, setFullNamesTranslator, sortBy, 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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

See Also

AffymetrixCelFile.

Examples

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 <- extract(ds, 1:min(3,nbrOfArrays(ds)))
print(ds)

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