DChipGenomeInformation: The DChipGenomeInformation class

Description

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.

Usage

DChipGenomeInformation(...)

Arguments

...

Arguments passed to GenomeInformation.

Fields and Methods

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, objectSize, print, save, asThis

Details

The dChip genome information files for various chip types can be downloaded from http://www.hsph.harvard.edu/cli/complab/dchip/. 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.