DChipGenomeInformation {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class DChipGenomeInformation
Object
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GenericDataFile
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GenomeInformation
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DChipGenomeInformation
Directly known subclasses:
public 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 . |
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.
Methods:
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:
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
Henrik Bengtsson (http://www.braju.com/R/)