AffymetrixCelFile: The AffymetrixCelFile class

Description

Package: aroma.affymetrix Class AffymetrixCelFile

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--CacheKeyInterface ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile

Directly known subclasses: ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class AffymetrixCelFile extends AffymetrixFile

An AffymetrixCelFile object represents a single Affymetrix CEL file.

Usage

AffymetrixCelFile(..., cdf=NULL)

Arguments

...

Arguments passed to AromaMicroarrayDataFile.

cdf

An optional AffymetrixCdfFile making it possible to override the default CDF file as specified by the CEL file header. The requirement is that its number of cells must match that of the CEL file. If NULL, the CDF structure is inferred from the the chip type as specified in the CEL file header.

Fields and Methods

Methods:

	`extractMatrix`
-
`getAm`	-
	`getCdf`
-
`getFileFormat`	-
	`getImage`
-
`getUnitNamesFile`	-
	`getUnitTypesFile`
-
`image270`	-
	`nbrOfCells`
-
`plotDensity`	-
	`plotImage`
-
`plotMvsA`	-
	`plotMvsX`
-
`setCdf`	-
	`smoothScatterMvsA`
-
`writeImage`	-

Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith 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, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, 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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

For developers

If you subclass this class, please make sure to query the AffymetrixCdfFile object (see *getCdf()) whenever querying CDF information. Do not use the CDF file inferred from the chip type in CEL header, unless you really want it to be hardwired that way, otherwise you will break to possibility to override the CDF structure.

Description

Usage

Arguments

Fields and Methods

For developers

See Also