AffymetrixPgfFile: The AffymetrixPgfFile class

Description

Package: aroma.affymetrix Class AffymetrixPgfFile Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--CacheKeyInterface ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaChipTypeAnnotationFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitNamesFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixPgfFile Directly known subclasses: public abstract static class AffymetrixPgfFile extends UnitNamesFile An AffymetrixPgfFile object represents a generic Affymetrix Probe Group File (PGF). A PGF file "provides information about what probes are contained within a probeset and information about the nature of the probes necessary for analysis. The current PGF file format (version 1) is only specified for expression style probesets." [1]

Usage

AffymetrixPgfFile(...)

Arguments

...

Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

Methods: rll{ getChipType - getDimension - getPlatform - getUnitNames Gets the names of each unit. nbrOfCells - nbrOfColumns - nbrOfRows - nbrOfUnits - }

Methods inherited from UnitNamesFile: getUnitNames, indexOf, nbrOfUnits

Methods inherited from UnitTypesFile: getUnitTypes, nbrOfUnits

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

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

Methods inherited from AromaChipTypeAnnotationFile: as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform

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

Methods inherited from FileCacheKeyInterface: getCacheKey

Methods inherited from CacheKeyInterface: getCacheKey

Methods inherited from GenericDataFile: as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, isGzipped, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName

Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

References

[1] ...