AffymetrixCdfFile {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class AffymetrixCdfFile
Object
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GenericDataFile
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AromaMicroarrayDataFile
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AffymetrixFile
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AromaChipTypeAnnotationFile
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AromaPlatformInterface
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UnitAnnotationDataFile
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UnitTypesFile
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UnitNamesFile
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AffymetrixCdfFile
Directly known subclasses:
public static class AffymetrixCdfFile
extends UnitNamesFile
An AffymetrixCdfFile object represents a generic Affymetrix CDF file.
AffymetrixCdfFile(...)
... |
Arguments passed to AromaChipTypeAnnotationFile . |
Methods:
convert | Converts a CDF into the same CDF but with another format. | |
createMonoCell | - | |
createUnique | - | |
getCellIndices | Gets the cell indices unit by unit. | |
getChipType | - | |
getDimension | - | |
getFileFormat | - | |
getGenomeInformation | Gets genome information for this chip type. | |
getImage | - | |
getMonoCell | - | |
getPlatform | - | |
getUnique | - | |
getUnitGroupNamesFromUgcMap | - | |
getUnitNames | Gets the names of each unit. | |
getUnitTypes | Gets the types of a set of units. | |
hasUnitTypes | - | |
isMonocellCdf | - | |
isPm | Checks which cells (probes) are PMs and not. | |
isUniqueCdf | - | |
nbrOfCells | - | |
nbrOfColumns | - | |
nbrOfQcUnits | - | |
nbrOfRows | - | |
nbrOfUnits | - | |
readDataFrame | - | |
readUnits | Reads CDF data unit by unit. | |
setGenomeInformation | - | |
setSnpInformation | - |
Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUgpFile, getChipType, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile
Methods inherited from AromaChipTypeAnnotationFile:
byChipType, byName, findByChipType, fromFile, getChipType, getHeader, getPlatform
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, hasAttributeXY, setAttributesByTags, setAttributeXY
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/)