Man pages for aroma.affymetrix
Analysis of Large Affymetrix Microarray Data Sets

AbstractProbeSequenceNormalizationThe AbstractProbeSequenceNormalization class
AdditiveCovariatesNormalizationThe AdditiveCovariatesNormalization class
AffineCnPlmThe AffineCnPlm class
AffinePlmThe AffinePlm class
AffineSnpPlmThe AffineSnpPlm class
AffymetrixCdfFileThe AffymetrixCdfFile class
AffymetrixCelFileThe AffymetrixCelFile class
AffymetrixCelSetThe AffymetrixCelSet class
AffymetrixCelSetReporterThe AffymetrixCelSetReporter class
AffymetrixCelSetTupleThe AffymetrixCelSetTuple class
AffymetrixCnChpSetThe AffymetrixCnChpSet class
AffymetrixFileThe abstract AffymetrixFile class
AffymetrixFileSetThe AffymetrixFileSet class
AffymetrixFileSetReporterThe AffymetrixFileSetReporter class
AffymetrixPgfFileThe AffymetrixPgfFile class
AffymetrixProbeTabFileThe AffymetrixProbeTabFile class
AlleleSummationThe AlleleSummation class
AllelicCrosstalkCalibrationThe AllelicCrosstalkCalibration class
allocateFromCdf.AffymetrixCelFileCreates an empty CEL file from a template CDF
allocateFromCdf.AromaUnitTabularBinaryFileCreates an AromaUnitTabularBinaryFile mapping to a given CDF
aroma.affymetrix-packagePackage aroma.affymetrix
AromaChipTypeAnnotationFileThe AromaChipTypeAnnotationFile class
ArrayExplorerThe ArrayExplorer class
as.AffymetrixCelSet.AffymetrixCelSetCoerce an object to an AffymetrixCelSet object
as.AffymetrixCnChpSet.AffymetrixCnChpSetCoerce an object to an AffymetrixCnChpSet object
as.AffymetrixFileSet.AffymetrixFileSetCoerce an object to an AffymetrixFileSet object
as.character.AffymetrixCelSetReturns a short string describing the Affymetrix CEL set
as.character.AffymetrixCnChpSetReturns a short string describing the set
as.character.CnagCfhSetReturns a short string describing the CNAG CFH set
as.character.DChipDcpSetReturns a short string describing the DChip CHP set
as.CnagCfhSet.CnagCfhSetCoerce an object to an CnagCfhSet object
as.DChipDcpSet.DChipDcpSetCoerce an object to an DChipDcpSet object
averageQuantile.AffymetrixCelSetCalculates the average empirical distribution across all...
AvgCnPlmThe AvgCnPlm class
AvgPlmThe AvgPlm class
AvgSnpPlmThe AvgSnpPlm class
BackgroundCorrectionThe BackgroundCorrection class
BaseCountNormalizationThe BaseCountNormalization class
BasePositionNormalizationThe BasePositionNormalization class
bpmapCluster2CdfCreates a CDF from tiling-array BPMAP file
byChipType.AromaChipTypeAnnotationFileDefines an AromaChipTypeAnnotationFile object by chip type
byChipType.DChipGenomeInformationDefines a DChipGenomeInformation object by chip type
byChipType.DChipSnpInformationDefines a DChipSnpInformation object by chip type
byChipType.GenomeInformationStatic method to define a genome information set by chip type
byChipType.SnpInformationStatic method to define a genome information set by chip type
byChipType.UgpGenomeInformationDefines a UgpGenomeInformation object by chip type
byPath.AffymetrixFileSetDefines an AffymetrixFileSet object by searching for...
calculateBaseline.ChipEffectSetEstimates the baseline signal chromosome by chromosome
calculateParametersGsb.AffymetrixCelSetComputes parameters for adjustment of specific binding
calculateResidualSet.FirmaModelGets the set of residuals corresponding to the PLM
ChipEffectFileThe ChipEffectFile class
ChipEffectGroupMergeThe ChipEffectGroupMerge class
ChipEffectSetThe ChipEffectSet class
ChipEffectTransformThe ChipEffectTransform class
clearData.AffymetrixCelFileClears all or a subset of the fields in a CEL file
CnagCfhFileThe CnagCfhFile class
CnagCfhSetThe CnagCfhSet class
CnChipEffectFileThe CnChipEffectFile class
CnChipEffectSetThe CnChipEffectSet class
CnPlmThe CnPlm class
CnProbeAffinityFileThe CnProbeAffinityFile class
compare.AffymetrixCdfFileChecks if two AffymetrixCdfFile objects are equal
computeAffinities.AffymetrixCdfFileCalculates probe affinities from sequence
convert.AffymetrixCdfFileConverts a CDF into the same CDF but with another format
convertUnits.AffymetrixCdfFileGets and validates unit indices
createExonByTranscriptCdf.AffymetrixCdfFileCreates an exon-by-transcript CDF
createFrom.AffymetrixCelFileCreates a CEL file using another as a template
createMonocellCdf.AffymetrixCdfFileCreates a mono-cell version of the CDF
createUniqueCdf.AffymetrixCdfFileCreates a unique-cell version of the CDF
CrlmmParametersFileThe CrlmmParametersFile class
CrlmmParametersSetThe CrlmmParametersSet class
DChipCdfBinFileThe DChipCdfBinFile class
DChipDcpFileThe DChipDcpFile class
DChipDcpSetThe DChipDcpSet class
DChipGenomeInformationThe DChipGenomeInformation class
DChipQuantileNormalizationThe DChipQuantileNormalization class
DChipSnpInformationThe DChipSnpInformation class
doCRMAv1Estimation and assessment of raw copy numbers at the single...
doCRMAv2A single-array preprocessing method for estimating...
doFIRMAFinding Isoforms using Robust Multichip Analysis (FIRMA)
doGCRMARobust Multichip Analysis (GCRMA)
doRMARobust Multichip Analysis (RMA)
ExonChipEffectFileThe ExonChipEffectFile class
ExonChipEffectSetThe ExonChipEffectSet class
ExonProbeAffinityFileThe ExonProbeAffinityFile class
ExonRmaPlmThe ExonRmaPlm class
extractAffyBatch.AffymetrixCelSetExtracts an in-memory AffyBatch object from the CEL set
extractDataFrame.ParameterCelSetExtract data as a data.frame for a set of arrays
extractExpressionSet.ChipEffectSetExtracts an in-memory ExpressionSet object
extractFeatureSet.AffymetrixCelSetExtracts CEL signals an in-memory FeatureSet object
extractMatrix.AffymetrixCelSetExtract data as a matrix for a set of arrays
extractMatrix.ParameterCelSetExtract data as a matrix for a set of arrays
findByChipType.AffymetrixCdfFileLocates a CDF file from its chip type
findByChipType.AffymetrixPgfFileLocates a PGF file from its chip type
findByChipType.AromaChipTypeAnnotationFileLocates an annotation file by its chip type
findUnitsTodo.FirmaModelIdentifies non-fitted units
findUnitsTodo.ProbeLevelModelIdentifies non-fitted units
findUnitsTodo.UnitModelIdentifies non-fitted units
FirmaFileThe FirmaFile class
FirmaModelThe FirmaModel class
FirmaSetThe FirmaSet class
fit.FirmaModelEstimates the model parameters
fit.ModelEstimates the model parameters
fit.ProbeLevelModelEstimates the model parameters
fitQuantileNormFcn.AffymetrixCelFileFits quantile normalization functions for the arrays in the...
fit.SingleArrayUnitModelEstimates the model parameters
fit.SmoothMultiarrayModelFits the model for one chromosome across samples
FragmentEquivalentClassNormalizationThe FragmentEquivalentClassNormalization class
FragmentLengthNormalizationThe FragmentLengthNormalization class
fromCdf.GenomeInformationStatic method to define a genome information set from a CDF
fromCdf.SnpInformationStatic method to define a genome information set from a CDF
fromDataFile.ChipEffectFileRetrive an existing CEL file, or create from CDF template if...
fromFile.AffymetrixCdfFileDefines an AffymetrixCdfFile object from a CDF file
fromFile.AffymetrixCelFileDefines an AffymetrixCelFile object from a CEL file
fromFile.AffymetrixPgfFileDefines an AffymetrixPgfFile object from a PGF file
fromFile.AromaChipTypeAnnotationFileSets up an AromaChipTypeAnnotationFile
fromFile.CnagCfhFileDefines an CnagCfhFile object from a CFH file
GcContentNormalizationThe GcContentNormalization class
GcContentNormalization2The GcContentNormalization2 class
GcRmaBackgroundCorrectionThe GcRmaBackgroundCorrection class
GenericReporterThe GenericReporter class
GenomeInformationThe GenomeInformation class
getAlias.GenericReporterGets the alias of the report
getAlias.ModelGets the name alias for the model
getAlleleCellPairs.AffymetrixCdfFileGets the cell indices of allele pairs
getAlleleProbePairs3.AffymetrixCdfFileGets the indices of probepairs with the same pair of SNP...
getAlleleProbePairs.AffymetrixCdfFileGets the indices of probepairs with the same pair of SNP...
getAM.ChipEffectFileGets the log-intensities and log-ratios of chip effects for...
getAM.ChipEffectSetGets the log-intensities and log-ratios of chip effects of...
getAverageFile.AffymetrixCelSetCalculates the mean and the standard deviation of the cell...
getAverageFile.CnagCfhSetCalculates the mean and the standard deviation of the cell...
getBaseline.ChipEffectSetGets the baseline signals across chromosomes
getCdf.AffymetrixCelFileGets the CDF structure for this CEL file
getCdf.AffymetrixCelSetGets the CDF structure for this CEL set
getCdf.CnagCfhFileGets the CDF structure for this CEL file
getCdf.CnagCfhSetGets the CDF structure for this CFH set
getCdf.ModelGets the CDF structure for this model
getCellIndices.AffymetrixCdfFileGets the cell indices unit by unit
getCellIndices.ChipEffectFileRetrieves tree list of cell indices for a set of units
getCellIndices.CnChipEffectFileRetrieves tree list of cell indices for a set of units
getCellIndices.CnProbeAffinityFileRetrieves tree list of cell indices for a set of units
getCellIndices.ExonChipEffectFileRetrieves tree list of cell indices for a set of units
getCellIndices.ExonProbeAffinityFileRetrieves tree list of cell indices for a set of units
getCellIndices.FirmaFileRetrieves tree list of cell indices for a set of units
getCellIndices.ProbeAffinityFileRetrieves tree list of cell indices for a set of units
getCellIndices.ResidualFileRetrieves tree list of cell indices for a set of units
getCellIndices.SnpChipEffectFileRetrieves tree list of cell indices for a set of units
getCellIndices.SnpProbeAffinityFileRetrieves tree list of cell indices for a set of units
getCellIndices.UnitModelGets the cell indices unit by unit
getCellIndices.WeightsFileRetrieves tree list of cell indices for a set of units
getChipEffectSet.AlleleSummationGets the set of chip effects for this model
getChipEffectSet.ProbeLevelModelGets the set of chip effects for this model
getChipType.AffymetrixCelFileGets the chip type for this CEL file
getChipType.AffymetrixCelSetGets the chip type for this CEL set
getChipType.CnagCfhFileGets the chip type for this CEL file
getChipType.GenomeInformationGets the chip type of this genome information set
getChipType.SnpInformationGets the chip type of this genome information set
getCnNames.AffymetrixCdfFileGets the names of the CN units
getData.GenomeInformationGets all or a subset of the genome information data
getDataSet.AffymetrixCelSetReporterGets the data set
getDataSet.ArrayExplorerGets the data set
getDataSet.ModelGets the input data set for this model
getData.SnpInformationGets all or a subset of the genome information data
getFirmaSet.FirmaModelGets the set of FIRMA results for this model
getFitUnitGroupFunction.AffinePlmGets the low-level function that fits the PLM
getFitUnitGroupFunction.AvgPlmGets the low-level function that fits the PLM
getFitUnitGroupFunction.ExonRmaPlmGets the low-level function that fits the Exon PLM
getFitUnitGroupFunction.FirmaModelStatic method to get the low-level function that fits the PLM
getFitUnitGroupFunction.HetLogAddPlmGets the low-level function that fits the PLM
getFitUnitGroupFunction.MbeiPlmGets the low-level function that fits the PLM
getFitUnitGroupFunction.MultiArrayUnitModelStatic method to get the low-level function that fits the PLM
getFitUnitGroupFunction.RmaPlmGets the low-level function that fits the PLM
getFitUnitGroupFunction.SingleArrayUnitModelStatic method to get the low-level function that fits the PLM
getFullName.ModelGets the full name of the output set
getFullName.TransformReportGets the full name of the output data set
getGenomeInformation.AffymetrixCdfFileGets genome information for this chip type
getHeader.AffymetrixCdfFileGets the header of the CDF file
getHeader.AffymetrixCelFileGets the header of the CEL file
getHeader.AffymetrixPgfFileGets the header of the PGF file
getHeader.AromaChipTypeAnnotationFileGets the header of the annotation file
getHeader.CnagCfhFileGets the header of the CEL file
getImage.AffymetrixCelFileCreates an RGB Image object from a CEL file
getInputDataSet.TransformReportGets the source data set
getIntensities.AffymetrixCelSetGets cell intensities from a set of cells and a set of arrays
getName.GenericReporterGets the name of the explorer
getName.ModelGets the name of the output data set
getName.TransformReportGets the name of the output data set
getOutputDataSet.TransformGets the transformed data set
getOutputDataSet.TransformReportGets the transformed data set
getPath.ModelGets the path of this model
getPath.TransformReportGets the path of the output data set
getPositions.GenomeInformationGets the physical positions for a set of units
getProbeAffinityFile.ProbeLevelModelGets the probe affinities for this model
getResiduals.QualityAssessmentModelCalculates the residuals from a probe-level model
getRootPath.ModelGets the root path of this model
getSnpNames.AffymetrixCdfFileGets the names of the SNP units
getTags.GenericReporterGets the tags of the reporter
getTags.ModelGets the tags of the output data set
getTags.TransformReportGets the tags of the output data set
getTimestamp.AffymetrixCelFileGets the timestamp in the CEL header
getUnitGroupCellMap.ChipEffectFileGets a (unit, group, cell) index map
getUnitIndices.GenomeInformationGets unit indices ordered along the chromosome
getUnitIntensities.AffymetrixCelSetGets cell signals for a subset of units and a subset of...
getUnitNames.AffymetrixCdfFileGets the names of each unit
getUnitNames.AffymetrixPgfFileGets the names of each unit
getUnitTypes.AffymetrixCdfFileGets the types of a set of units
getWeights.QualityAssessmentModelCalculates the weights from the robust fit to a probe-level...
getXAM.ChipEffectFileGets the physical position, log-intensities and log-ratios of...
getXAM.ChipEffectSetGets the physical position, log-intensities and log-ratios of...
groupUnitsByDimension.AffymetrixCdfFileGroups units by dimensions
HetLogAddCnPlmThe HetLogAddCnPlm class
HetLogAddPlmThe HetLogAddPlm class
HetLogAddSnpPlmThe HetLogAddSnpPlm class
image270.AffymetrixCelFileDisplays all or a subset of the data spatially
importFromApt.CnChipEffectSetImports copy-number estimates from an APT summary file
importFromDChip.AffymetrixCelSetImports dChip-exported CEL files
importFromDChip.CnChipEffectSetImports copy-number estimates from a dChip result file
isDuplicated.AffymetrixCelSetIdentifies duplicated CEL files
isDuplicated.CnagCfhSetIdentifies duplicated CFH files
isPm.AffymetrixCdfFileChecks which cells (probes) are PMs and not
isResequenceChip.AffymetrixCdfFileStatic method to check if a CDF is for a resequencing...
isSnpChip.AffymetrixCdfFileStatic method to check if a chip is a mapping (SNP) chip
justRMARobust Multichip Analysis (RMA) reproducing the affy package
LimmaBackgroundCorrectionThe LimmaBackgroundCorrection class
LinearModelProbeSequenceNormalizationThe LinearModelProbeSequenceNormalization class
MatNormalizationThe MatNormalization class
MatSmoothingThe MatSmoothing class
MbeiCnPlmThe MbeiCnPlm class
MbeiPlmThe MbeiPlm class
MbeiSnpPlmThe MbeiSnpPlm class
ModelThe Model class
MultiArrayUnitModelThe MultiArrayUnitModel class
nbrOfArrays.AffymetrixCelSetGets the number of arrays in the file set
nbrOfGroupsPerUnit.AffymetrixCdfFileGets the number of groups in each unit
nbrOfSnps.AffymetrixCdfFileGets the number of SNPs
Non-documented_objectsNon-documented objects
normalizeQuantile.AffymetrixCelFileNormalizes the probe intensities to a target empirical...
normalizeQuantile.AffymetrixCelSetNormalizes samples to have the same empirical distribution
NormExpBackgroundCorrectionThe NormExpBackgroundCorrection class
OpticalBackgroundCorrectionThe OpticalBackgroundCorrection class
ParameterCelFileThe ParameterCelFile class
ParameterCelSetThe ParameterCelSet class
pdInfo2CdfGenerates an Affymetrix CDF file from a Platform Design (PD)...
plotBoxplotStats.listPlots a (merged or non-merged) list of boxplot.stats()...
plotDensity.AffymetrixCelFilePlots the density of the probe signals on the array
plotDensity.AffymetrixCelSetPlots the densities of all samples
plotDensity.GenomeInformationPlots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFileDisplays a spatial plot of a CEL file
plotMvsA.AffymetrixCelFilePlots log-ratio versus log-intensity in a scatter plot
plotMvsX.AffymetrixCelFilePlots log-ratio versus another variable in a scatter plot
ProbeAffinityFileThe ProbeAffinityFile class
ProbeLevelModelThe ProbeLevelModel class
ProbeLevelTransformThe ProbeLevelTransform class
ProbeLevelTransform3The ProbeLevelTransform3 class
process.AbstractProbeSequenceNormalizationNormalizes the data set
process.AdditiveCovariatesNormalizationNormalizes the data set
process.AllelicCrosstalkCalibrationCalibrates the data set
process.ArrayExplorerGenerates image files, scripts and dynamic pages for the...
process.BackgroundCorrectionProcesses the data set
process.ChipEffectGroupMergeNormalizes the data set
process.DChipQuantileNormalizationNormalizes the data set
process.FragmentEquivalentClassNormalizationNormalizes the data set
process.FragmentLengthNormalizationNormalizes the data set
process.GcContentNormalizationNormalizes the data set
process.GcRmaBackgroundCorrectionPerforms background correction
process.GenericReporterGenerates report
process.LimmaBackgroundCorrectionPerforms background correction
process.MatNormalizationNormalizes the data set
process.MatSmoothingProcesses the data set
process.OpticalBackgroundCorrectionPerforms background correction
process.QuantileNormalizationNormalizes the data set
process.ReseqCrosstalkCalibrationCalibrates the data set
process.RmaBackgroundCorrectionPerforms background correction
process.ScaleNormalizationNormalizes the data set
process.ScaleNormalization3Normalizes the data set
process.SpatialReporterGenerates image files, scripts and dynamic pages for the...
process.UnitTypeScaleNormalizationNormalizes the data set
QualityAssessmentFileThe QualityAssessmentFile class
QualityAssessmentModelThe QualityAssessmentModel class
QualityAssessmentSetThe QualityAssessmentSet class
QuantileNormalizationThe QuantileNormalization class
randomSeedSets and resets the .Random.seed in the global environment
readRawData.AffymetrixCelFileGets all or a subset of the fields in a CEL file
readUnits.AffymetrixCdfFileReads CDF data unit by unit
readUnits.AffymetrixCelFileReads CEL data unit by unit
readUnitsByQuartets.AffymetrixCdfFileGets the cell quartets for each base position
readUnits.CnagCfhFileReads CEL data unit by unit
readUnits.MultiArrayUnitModelReads data unit by unit
readUnits.SingleArrayUnitModelReads data unit by unit
ReseqCrosstalkCalibrationThe ReseqCrosstalkCalibration class
ResidualFileThe ResidualFile class
ResidualSetThe ResidualSet class
RmaBackgroundCorrectionThe RmaBackgroundCorrection class
RmaCnPlmThe RmaCnPlm class
RmaPlmThe RmaPlm class
RmaSnpPlmThe RmaSnpPlm class
ScaleNormalizationThe ScaleNormalization class
ScaleNormalization3The ScaleNormalization3 class
setAlias.GenericReporterSets the alias of the report
setAlias.ModelSets the name alias for the model
setArrays.ArrayExplorerSets the arrays
setCdf.AffymetrixCelFileSets the CDF structure for this CEL file
setCdf.AffymetrixCelSetSets the CDF structure for this CEL set
setCdf.CnagCfhFileSets the CDF structure for this CEL file
setCdf.CnagCfhSetSets the CDF structure for this CFH set
setRestructor.AffymetrixCdfFileSpecifies a function through which
setTags.ModelSets the tags to be appended
setupExampleDataSetups example data in the current directory
setupExampleData.AromaAffymetrixSetups example data in the current directory
SingleArrayUnitModelThe SingleArrayUnitModel class
SmoothMultiarrayModelThe SmoothMultiarrayModel class
SmoothRmaModelThe SmoothRmaModel class
smoothScatterMvsA.AffymetrixCelFilePlots log-ratio versus log-intensity in a smooth scatter plot
SnpChipEffectFileThe SnpChipEffectFile class
SnpChipEffectGroupMergeThe SnpChipEffectGroupMerge class
SnpChipEffectSetThe SnpChipEffectSet class
SnpInformationThe SnpInformation class
SnpPlmThe SnpPlm interface class
SnpProbeAffinityFileThe SnpProbeAffinityFile class
SpatialReporterThe SpatialReporter class
TransformReportThe TransformReport class
UgpGenomeInformationThe UgpGenomeInformation class
UnitModelThe UnitModel class
UnitTypeScaleNormalizationThe UnitTypeScaleNormalization class
updateUnits.AffymetrixCelFileUpdates CEL data unit by unit
verify.GenomeInformationVerifies the correctness of the underlying file
verify.SnpInformationVerifies the correctness of the underlying file
WeightsFileThe WeightsFile class
WeightsSetThe WeightsSet class
writeCdf.AffyGenePDInfoGenerates an Affymetrix CDF file from a Platform Design (PD)...
writeImage.AffymetrixCelFileWrites a spatial image of the signals in the CEL file
aroma.affymetrix documentation built on May 29, 2017, 9:47 a.m.