AffymetrixCdfFile: The AffymetrixCdfFile class
Description
Package: aroma.affymetrix
Class AffymetrixCdfFile
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--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.Usage
AffymetrixCdfFile(...)
Fields and Methods
Methods:
rll{
convert Converts a CDF into the same CDF but with another format.
createMonoCell -
getACSFile -
getAromaCellSequenceFile -
getCellIndices Gets the cell indices unit by unit.
getChipType -
getDimension -
getFileFormat -
getGenomeInformation Gets genome information for this chip type.
getImage -
getMonoCell -
getPlatform -
getUnitGroupNamesFromUgcMap -
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.
setGenomeInformation -
setSnpInformation -
}
Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaChipTypeAnnotationFile:
byChipType, byName, findByChipType, fromFile, getChipType, getHeader, getPlatform
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributesByTags, setAttributeXY
Methods inherited from GenericDataFile:
getParentName, compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save