AffymetrixCelFile {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class AffymetrixCelFile
Object
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GenericDataFile
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AromaMicroarrayDataFile
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AromaPlatformInterface
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AffymetrixFile
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AffymetrixCelFile
Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile
public static class AffymetrixCelFile
extends AffymetrixFile
An AffymetrixCelFile object represents a single Affymetrix CEL file.
AffymetrixCelFile(..., cdf=NULL)
... |
Arguments passed to AromaMicroarrayDataFile . |
cdf |
An optional AffymetrixCdfFile making it possible to
override the default CDF file as specified by the CEL file header.
The requirement is that its number of cells must match that of
the CEL file.
If NULL , the CDF structure is inferred from the the chip type
as specified in the CEL file header. |
Methods:
[ | - | |
[[ | - | |
clone | - | |
extractMatrix | - | |
fromFile | Defines an AffymetrixCelFile object from a CEL file. | |
getAm | - | |
getCdf | Gets the CDF structure for this CEL file. | |
getFileFormat | - | |
getImage | Creates an RGB Image object from a CEL file. | |
getUnitNamesFile | - | |
getUnitTypesFile | - | |
highlight | - | |
image270 | Displays all or a subset of the data spatially. | |
nbrOfCells | - | |
plotDensity | Plots the density of the probe signals on the array. | |
plotImage | Displays a spatial plot of a CEL file. | |
plotMvsA | Plots log-ratio versus log-intensity in a scatter plot. | |
plotMvsX | Plots log-ratio versus another variable in a scatter plot. | |
setCdf | Sets the CDF structure for this CEL file. | |
smoothScatterMvsA | Plots log-ratio versus log-intensity in a smooth scatter plot. | |
writeImage | Writes a spatial image of the signals in the CEL file. |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile
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
If you subclass this class, please make sure to query the
AffymetrixCdfFile
object (see *getCdf()
) whenever
querying CDF information. Do not use the CDF file inferred from the
chip type in CEL header, unless you really want it to be hardwired that
way, otherwise you will break to possibility to override the CDF
structure.
Henrik Bengtsson (http://www.braju.com/R/)
An object of this class is typically part of an AffymetrixCelSet
.