GenomeInformation: The GenomeInformation class

Description

Package: aroma.affymetrix Class GenomeInformation

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--CacheKeyInterface ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--GenomeInformation

Directly known subclasses: AffymetrixCsvGenomeInformation, DChipGenomeInformation, UgpGenomeInformation

public abstract static class GenomeInformation extends FileCacheKeyInterface

Usage

GenomeInformation(..., .verify=TRUE)

Arguments

...

Arguments passed to GenericDataFile.

.verify

For internal use only.

Fields and Methods

Methods:

	`byChipType`
-
`getChipType`	-
	`getChromosomeStats`
-
`getChromosomes`	-
	`getData`
-
`getPositions`	-
	`getUnitsOnChromosome`
-
`getUnitsOnChromosomes`	-
	`nbrOfUnits`
-
`plotDensity`	-

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