AffymetrixCelSet {aroma.affymetrix}R Documentation

The AffymetrixCelSet class

Description

Package: aroma.affymetrix
Class AffymetrixCelSet

Object
~~|
~~+--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:
[ -
[[ -
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.
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 -
getFullName -
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, fromFiles

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, as.list, byName, clearCache, copyTo, equals, extract, findByName, fromFiles, getAlias, getFile, getFileClass, getFileSize, getFullName, getFullNames, getFullNameTranslator, getName, getNames, getPath, getPathnames, getTags, hasFile, hasTag, hasTags, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullName, setFullNamesTranslator, setFullNameTranslator, setName, setTags, update2, validate

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

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

AffymetrixCelFile.

Examples

## Not run: 
   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)

 ## End(Not run)

[Package aroma.affymetrix version 1.2.0 Index]