Package: aroma.affymetrix
Class DChipGenomeInformation
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--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.
DChipGenomeInformation(...)
Arguments passed to GenomeInformation.
Methods:
byChipType | - | |
readDataFrame | - |
Methods inherited from GenomeInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getChromosomeStats, getChromosomes, getData, getPositions, getUnitIndices, getUnitsOnChromosome, getUnitsOnChromosomes, isCompatibleWithCdf, nbrOfUnits, plotDensity, readDataFrame, verify
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
Henrik Bengtsson
The dChip genome information files for various chip types can be
downloaded from https://sites.google.com/site/dchipsoft/.
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.