Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaChipTypeAnnotationFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCdfFile
Directly known subclasses:
public abstract static class AffymetrixCdfFile
extends UnitNamesFile
An AffymetrixCdfFile object represents a generic Affymetrix CDF file.AffymetrixCdfFile(...)AromaChipTypeAnnotationFile.convert Converts a CDF into the same CDF but with another format.
createExonByTranscriptCdf Creates an exon-by-transcript CDF.
getACSFile -
getAromaCellSequenceFile -
getCellIndices Gets the cell indices unit by unit.
getChipType -
getDimension -
getFileFormat -
getGenomeInformation Gets genome information for this chip type.
getImage -
getPlatform -
getUnitNames Gets the names of each unit.
getUnitTypes Gets the types of a set of units.
hasUnitTypes -
isMonocellCdf -
isPm Checks which cells (probes) are PMs and not.
isUniqueCdf -
nbrOfCells -
nbrOfColumns -
nbrOfQcUnits -
nbrOfRows -
nbrOfUnits -
readDataFrame -
readUnits Reads CDF data unit by unit.
}Methods inherited from UnitNamesFile: getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitTypesFile: getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile: byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaChipTypeAnnotationFile: as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform
Methods inherited from AromaMicroarrayDataFile: getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface: getCacheKey
Methods inherited from CacheKeyInterface: getCacheKey
Methods inherited from GenericDataFile: as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, isGzipped, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, 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