GenomeInformation: The GenomeInformation class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

GenomeInformation

R Documentation

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`	Static method to define a genome information set by chip type.
	`getChipType`	Gets the chip type of this genome information set.
	`getChromosomeStats`	-
	`getChromosomes`	-
	`getData`	Gets all or a subset of the genome information data.
	`getPositions`	Gets the physical positions for a set of units.
	`getUnitsOnChromosome`	-
	`getUnitsOnChromosomes`	-
	`nbrOfUnits`	-
	`plotDensity`	Plots the density of SNPs for a given chromosome.

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, names, objectSize, print, save, asThis