ParameterCelFile {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class ParameterCelFile
Object
~~|
~~+--
GenericDataFile
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~~~~~~~+--
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/)