ExonChipEffectFile {aroma.affymetrix}R Documentation

The ExonChipEffectFile class

Description

Package: aroma.affymetrix
Class ExonChipEffectFile

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

Directly known subclasses:

public static class ExonChipEffectFile
extends ChipEffectFile

This class represents estimates of chip effects in the probe-level models.

Usage

ExonChipEffectFile(..., mergeGroups=FALSE)

Arguments

... Arguments passed to ChipEffectFile.
mergeGroups Specifies if the groups are merged or not for these estimates.

Fields and Methods

Methods:
getCellIndices -
getParameters -
readUnits -

Methods inherited from ChipEffectFile:
extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellChromosomePositionMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, getParameters, 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

Author(s)

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

See Also

An object of this class is typically part of a ExonChipEffectSet.


[Package aroma.affymetrix version 1.2.0 Index]