AffymetrixCelFile: The AffymetrixCelFile class
Description
Package: aroma.affymetrix
Class AffymetrixCelFile
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile
public abstract static class AffymetrixCelFile
extends AffymetrixFile
An AffymetrixCelFile object represents a single Affymetrix CEL file.Usage
AffymetrixCelFile(..., cdf=NULL)
Arguments
cdf
An optional AffymetrixCdfFile making it possible to
override the default CDF file as specified by the CEL file header.
The requirement is that its number of cells must match that of
Fields and Methods
Methods:
rll{
[ -
[[ -
clone -
extractMatrix -
fromFile Defines an AffymetrixCelFile object from a CEL file.
getAm -
getCdf Gets the CDF structure for this CEL file.
getFileFormat -
getImage Creates an RGB Image object from a CEL file.
getUnitNamesFile -
getUnitTypesFile -
highlight -
image270 Displays all or a subset of the data spatially.
nbrOfCells -
plotDensity Plots the density of the probe signals on the array.
plotImage Displays a spatial plot of a CEL file.
plotMvsA Plots log-ratio versus log-intensity in a scatter plot.
plotMvsX Plots log-ratio versus another variable in a scatter plot.
setCdf Sets the CDF structure for this CEL file.
smoothScatterMvsA Plots log-ratio versus log-intensity in a smooth scatter plot.
writeImage Writes a spatial image of the signals in the CEL file.
}
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
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, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
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, saveFor developers
If you subclass this class, please make sure to query the
AffymetrixCdfFile object (see *getCdf()) whenever
querying CDF information. Do not use the CDF file inferred from the
chip type in CEL header, unless you really want it to be hardwired that
way, otherwise you will break to possibility to override the CDF
structure.