ParameterCelFile: The ParameterCelFile class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

ParameterCelFile

R Documentation

The ParameterCelFile class

Description

Package: aroma.affymetrix
Class ParameterCelFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile

Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ProbeAffinityFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class ParameterCelFile
extends ParametersInterface

A ParameterCelFile object represents parameter estimates.

Usage

ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)

Arguments

`...`	Arguments passed to `AffymetrixCelFile`.
`encodeFunction`	A `function` taking a single `list` structure as its argument.
`decodeFunction`	A `function` taking a single `list` structure as its argument.

Fields and Methods

Methods:

	`extractDataFrame`	-
	`extractMatrix`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

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, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, 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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

File format

The idea behind this class is store data fields which by nature have one value per probe (per field) in CEL files. A perfect example is to store probe-affinity estimates and their standard deviations. There is one probe affinity per probe so the structure of a CEL file (and its coupled CDF file) is well suited to read/write such information.

Consider a unit group with L probes. A CEL file stores intensities (L floats), stdvs (L floats), and pixels (L integers). Thus, for each probe l=1,...,L, a (float, float, integer) tuple is stored. We can use this for any information we want. If we want a slightly different structure, we can choose to encode/decode our structure/information to fit the structure of the CEL file. This abstract class provides transparent methods for encoding and decoding such information through methods encodeUnitGroup() and decodeUnitGroup(). By subclassing you can implement different types of data structures.