| ParameterCelFile {aroma.affymetrix} | R Documentation |
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.
ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)
... |
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. |
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
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.
Henrik Bengtsson (http://www.braju.com/R/)