AffymetrixCdfFile {aroma.affymetrix}R Documentation

The AffymetrixCdfFile class

Description

Package: aroma.affymetrix
Class AffymetrixCdfFile

Object
~~|
~~+--GenericDataFile
~~~~~~~|
~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaChipTypeAnnotationFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCdfFile

Directly known subclasses:

public static class AffymetrixCdfFile
extends UnitNamesFile

An AffymetrixCdfFile object represents a generic Affymetrix CDF file.

Usage

AffymetrixCdfFile(...)

Arguments

... Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

Methods:
convert Converts a CDF into the same CDF but with another format.
createMonoCell -
createUnique -
getCellIndices Gets the cell indices unit by unit.
getChipType -
getDimension -
getFileFormat -
getGenomeInformation Gets genome information for this chip type.
getImage -
getMonoCell -
getPlatform -
getUnique -
getUnitGroupNamesFromUgcMap -
getUnitNames Gets the names of each unit.
getUnitTypes Gets the types of a set of units.
hasUnitTypes -
isMonocellCdf -
isPm Checks which cells (probes) are PMs and not.
isUniqueCdf -
nbrOfCells -
nbrOfColumns -
nbrOfQcUnits -
nbrOfRows -
nbrOfUnits -
readDataFrame -
readUnits Reads CDF data unit by unit.
setGenomeInformation -
setSnpInformation -

Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits

Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUgpFile, getChipType, getPlatform, nbrOfUnits

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

Methods inherited from AromaChipTypeAnnotationFile:
byChipType, byName, findByChipType, fromFile, getChipType, getHeader, getPlatform

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/)


[Package aroma.affymetrix version 1.2.0 Index]