DChipGenomeInformation: The DChipGenomeInformation class
Description
Package: aroma.affymetrix
Class DChipGenomeInformation
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenomeInformation
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--DChipGenomeInformation
Directly known subclasses:
public abstract static class DChipGenomeInformation
extends GenomeInformation
This class represents dChip genome information files, which typically
contains information about chromosomal locations of the units.Usage
DChipGenomeInformation(...)
Fields and Methods
Methods:
rll{
byChipType Defines a DChipGenomeInformation object by chip type.
readDataFrame -
}
Methods inherited from GenomeInformation:
byChipType, fromCdf, fromDataSet, getChipType, getChromosomes, getChromosomeStats, getData, getPositions, getUnitIndices, getUnitsOnChromosome, getUnitsOnChromosomes, isCompatibleWithCdf, nbrOfUnits, plotDensity, readDataFrame
Methods inherited from GenericDataFile:
getParentName, compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
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, saveDetails
The dChip genome information files for various chip types can be
downloaded from http://www.dchip.org/. Put each file in a
directory named identically as the corresponding chip type under the
annotations/ directory, e.g.
annotations/Mapping50K_Hind240/50k hind genome info AfAm
june 05 hg17.xls.
Note that dChip changes the filename and file format slightly between
chip types, but currently the *byChipType() basically searches
for files with names consisting of "genome info" or
"genome_info". At least for the most common chip types, there
is no need to rename the files in order for this class to recognize them.