GenomeInformation {aroma.affymetrix}R Documentation

The GenomeInformation class

Description

Package: aroma.affymetrix
Class GenomeInformation

Object
~~|
~~+--GenericDataFile
~~~~~~~|
~~~~~~~+--GenomeInformation

Directly known subclasses:
AffymetrixCsvGenomeInformation, DChipGenomeInformation, UgpGenomeInformation

public abstract static class GenomeInformation
extends GenericDataFile

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.
fromCdf Static method to define a genome information set from a CDF.
fromDataSet -
getChipType Gets the chip type of this genome information set.
getChromosomes -
getChromosomeStats -
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 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]