CnChipEffectFile {aroma.affymetrix} | R Documentation |
Package: aroma.affymetrix
Class CnChipEffectFile
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
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ParameterCelFile
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ChipEffectFile
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SnpChipEffectFile
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CnChipEffectFile
Directly known subclasses:
public static class CnChipEffectFile
extends SnpChipEffectFile
This class represents estimates of chip effects in a copy-number probe-level models.
CnChipEffectFile(..., combineAlleles=FALSE)
... |
Arguments passed to SnpChipEffectFile . |
combineAlleles |
A logical indicating if the signals from allele A
and allele B are combined or not. |
Methods:
exportAromaSignalBinaryFileList | - | |
exportTotalAndFracB | - | |
extractTheta | - | |
extractTotalAndFreqB | - | |
getCellIndices | - | |
getExpandedCellMap | - | |
getParameters | - | |
mergeStrands | - | |
readUnits | - |
Methods inherited from SnpChipEffectFile:
exportTotalAndFracB, extractCNT, extractTheta, extractTotalAndFracB, getCellIndices, getExpandedCellMap, getParameters, mergeStrands, readUnits, writeCNT
Methods inherited from ChipEffectFile:
extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellChromosomePositionMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, getParameters, readUnits
Methods inherited from AffymetrixCelFile:
[, [[, allocateFromCdf, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, setCdf, smoothScatterMvsA, writeImage
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
Henrik Bengtsson (http://www.braju.com/R/)
An object of this class is typically part of a CnChipEffectSet
.