aroma.affymetrix (version 1.3.0)

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{ [ - [[ - append - as - as.AffymetrixCelSet Coerce an object to an AffymetrixCelSet object. byName - convertToUnique - extractAffyBatch Extracts an in-memory AffyBatch object from the CEL set. extractMatrix Extract data as a matrix for a set of arrays. extractSnpFeatureSet - findByName - 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 - isDuplicated Identifies duplicated CEL files. justSNPRMA - nbrOfArrays Gets the number of arrays in the file set. plotDensity Plots the densities of all samples. range - 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, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile Methods inherited from AromaMicroarrayDataSet: getChipType, getPlatform, nbrOfArrays, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate Methods inherited from GenericDataFileSet: append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, appendFullNamesTranslatorByNULL, as.list, byName, byPath, clearCache, clearFullNamesTranslator, copyTo, equals, extract, findByName, fromFiles, getAlias, getDefaultFullName, getFile, getFileClass, getFileSize, getFullNames, getNames, getPath, getPathnames, hasFile, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullNamesTranslator, update2, updateFullName, updateFullNames, validate Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName Methods inherited from Object: asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

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)