AffymetrixCelSet | R Documentation |
Package: aroma.affymetrix
Class AffymetrixCelSet
Object
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~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
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~~~~~~~~~~~~+--
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.
AffymetrixCelSet(files=NULL, ...)
files |
A |
... |
Not used. |
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:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
AffymetrixCelFile
.
## Not run:
for (zzz in 0) {
# Find any dataset
path <- NULL
if (is.null(path))
break
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define a dataset object based on all CEL files in a directory
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ds <- AffymetrixCelSet$fromFiles(path)
print(ds)
# Keep at most three arrays for this example
ds <- ds[1:min(3,nbrOfArrays(ds))]
print(ds)
} # for (zzz in 0)
rm(zzz)
## End(Not run)
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