AffymetrixCelSet {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class AffymetrixCelSet
Object
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GenericDataFileSet
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AromaMicroarrayDataSet
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AromaPlatformInterface
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AffymetrixFileSet
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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 list of AffymetrixCelFile :s. |
... |
Not used. |
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, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Henrik Bengtsson (http://www.braju.com/R/)
## Not run: for (zzz in 0) { # Find any dataset path <- NULL if (is.null(path)) break # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define a dataset object based on all CEL files in a directory # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ds <- AffymetrixCelSet$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)