ParameterCelFile {aroma.affymetrix}R Documentation

The ParameterCelFile class

Description

Package: aroma.affymetrix
Class ParameterCelFile

Object
~~|
~~+--GenericDataFile
~~~~~~~|
~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile

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

public static class ParameterCelFile
extends AffymetrixCelFile

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 AffymetrixCelFile:
[, [[, allocateFromCdf, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, setCdf, smoothScatterMvsA, writeImage

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, hasAttributeXY, setAttributesByTags, setAttributeXY

Methods inherited from GenericDataFile:
compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getFilename, getFileSize, getFileType, getFullName, getFullNameTranslator, getLastAccessedOn, getLastModifiedOn, getName, getPath, getPathname, getTags, gunzip, gzip, hasBeenModified, hasTag, hasTags, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setFullName, setFullNameTranslator, setName, testAttributes, validateChecksum, writeChecksum

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

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.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.affymetrix version 1.2.0 Index]