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aroma.affymetrix (version 3.2.2)

Analysis of Large Affymetrix Microarray Data Sets

Description

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

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Install

install.packages('aroma.affymetrix')

Monthly Downloads

818

Version

3.2.2

License

LGPL (>= 2.1)

Issues

9

Pull Requests

0

Stars

10

Forks

3

Maintainer

Henrik Bengtsson

Last Published

February 18th, 2024

Functions in aroma.affymetrix (3.2.2)

AffineCnPlm

The AffineCnPlm class
AffinePlm

The AffinePlm class
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
AromaChipTypeAnnotationFile

The AromaChipTypeAnnotationFile class
ArrayExplorer

The ArrayExplorer class
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
AffymetrixCnChpSet

The AffymetrixCnChpSet class
AvgSnpPlm

The AvgSnpPlm class
BackgroundCorrection

The BackgroundCorrection class
AffymetrixFile

The abstract AffymetrixFile class
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
ChipEffectSet

The ChipEffectSet class
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
AffymetrixPgfFile

The AffymetrixPgfFile class
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
BaseCountNormalization

The BaseCountNormalization class
ChipEffectTransform

The ChipEffectTransform class
CnPlm

The CnPlm class
BasePositionNormalization

The BasePositionNormalization class
CnProbeAffinityFile

The CnProbeAffinityFile class
FirmaFile

The FirmaFile class
FirmaModel

The FirmaModel class
FirmaSet

The FirmaSet class
AffymetrixCelFile

The AffymetrixCelFile class
AffymetrixCelSet

The AffymetrixCelSet class
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
MbeiPlm

The MbeiPlm class
AvgCnPlm

The AvgCnPlm class
AvgPlm

The AvgPlm class
ExonProbeAffinityFile

The ExonProbeAffinityFile class
DChipCdfBinFile

The DChipCdfBinFile class
CnagCfhFile

The CnagCfhFile class
CnagCfhSet

The CnagCfhSet class
DChipDcpSet

The DChipDcpSet class
DChipDcpFile

The DChipDcpFile class
ExonRmaPlm

The ExonRmaPlm class
AffymetrixFileSet

The AffymetrixFileSet class
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
DChipGenomeInformation

The DChipGenomeInformation class
CnChipEffectFile

The CnChipEffectFile class
CnChipEffectSet

The CnChipEffectSet class
FragmentLengthNormalization

The FragmentLengthNormalization class
LinearModelProbeSequenceNormalization

The LinearModelProbeSequenceNormalization class
MbeiSnpPlm

The MbeiSnpPlm class
GcContentNormalization

The GcContentNormalization class
DChipQuantileNormalization

The DChipQuantileNormalization class
ProbeLevelTransform3

The ProbeLevelTransform3 class
HetLogAddCnPlm

The HetLogAddCnPlm class
HetLogAddPlm

The HetLogAddPlm class
MatNormalization

The MatNormalization class
Model

The Model class
Non-documented objects

Non-documented objects
ParameterCelSet

The ParameterCelSet class
QualityAssessmentFile

The QualityAssessmentFile class
ProbeAffinityFile

The ProbeAffinityFile class
QualityAssessmentModel

The QualityAssessmentModel class
MultiArrayUnitModel

The MultiArrayUnitModel class
QualityAssessmentSet

The QualityAssessmentSet class
QuantileNormalization

The QuantileNormalization class
RmaBackgroundCorrection

The RmaBackgroundCorrection class
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
ReseqCrosstalkCalibration

The ReseqCrosstalkCalibration class
SingleArrayUnitModel

The SingleArrayUnitModel class
RmaCnPlm

The RmaCnPlm class
DChipSnpInformation

The DChipSnpInformation class
ScaleNormalization

The ScaleNormalization class
SmoothMultiarrayModel

The SmoothMultiarrayModel class
GcContentNormalization2

The GcContentNormalization2 class
SnpChipEffectSet

The SnpChipEffectSet class
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
WeightsFile

The WeightsFile class
NormExpBackgroundCorrection

The NormExpBackgroundCorrection class
SmoothRmaModel

The SmoothRmaModel class
ScaleNormalization3

The ScaleNormalization3 class
SnpChipEffectFile

The SnpChipEffectFile class
WeightsSet

The WeightsSet class
TransformReport

The TransformReport class
SnpProbeAffinityFile

The SnpProbeAffinityFile class
HetLogAddSnpPlm

The HetLogAddSnpPlm class
LimmaBackgroundCorrection

The LimmaBackgroundCorrection class
SpatialReporter

The SpatialReporter class
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
bpmapCluster2Cdf

Creates a CDF from tiling-array BPMAP file
as.character.AffymetrixCelSet

Returns a short string describing the Affymetrix CEL set
as.character.AffymetrixCnChpSet

Returns a short string describing the set
ParameterCelFile

The ParameterCelFile class
RmaPlm

The RmaPlm class
AffymetrixCelFile$clearData

Clears all or a subset of the fields in a CEL file
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
UgpGenomeInformation

The UgpGenomeInformation class
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
RmaSnpPlm

The RmaSnpPlm class
compare.AffymetrixCdfFile

Checks if two AffymetrixCdfFile objects are equal
byChipType.DChipSnpInformation

Defines a DChipSnpInformation object by chip type
GenomeInformation$byChipType

Static method to define a genome information set by chip type
SnpInformation

The SnpInformation class
SnpPlm

The SnpPlm interface class
aroma.affymetrix-package

Package aroma.affymetrix
as.AffymetrixCelSet.AffymetrixCelSet

Coerce an object to an AffymetrixCelSet object
AffymetrixCelFile$allocateFromCdf

Creates an empty CEL file from a template CDF
createUniqueCdf.AffymetrixCdfFile

Creates a unique-cell version of the CDF
AffineSnpPlm

The AffineSnpPlm class
AffymetrixFileSet$byPath

Defines an AffymetrixFileSet object by searching for Affymetrix files
AffymetrixCdfFile

The AffymetrixCdfFile class
AromaUnitTabularBinaryFile$allocateFromCdf

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
doCRMAv1

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
AffymetrixCelFile$fromFile

Defines an AffymetrixCelFile object from a CEL file
AlleleSummation

The AlleleSummation class
AromaChipTypeAnnotationFile$byChipType

Defines an AromaChipTypeAnnotationFile object by chip type
AffymetrixPgfFile$fromFile

Defines an AffymetrixPgfFile object from a PGF file
as.AffymetrixCnChpSet.AffymetrixCnChpSet

Coerce an object to an AffymetrixCnChpSet object
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
getCdf.AffymetrixCelSet

Gets the CDF structure for this CEL set
doGCRMA

Robust Multichip Analysis (GCRMA)
extractMatrix.AffymetrixCelSet

Extract data as a matrix for a set of arrays
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
byChipType.SnpInformation

Static method to define a genome information set by chip type
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
UgpGenomeInformation$byChipType

Defines a UgpGenomeInformation object by chip type
convertUnits.AffymetrixCdfFile

Gets and validates unit indices
ChipEffectFile

The ChipEffectFile class
getCellIndices.CnProbeAffinityFile

Retrieves tree list of cell indices for a set of units
ChipEffectGroupMerge

The ChipEffectGroupMerge class
ChipEffectFile$fromDataFile

Retrieve an existing CEL file, or create from CDF template if missing
CrlmmParametersFile

The CrlmmParametersFile class
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
getCellIndices.ExonChipEffectFile

Retrieves tree list of cell indices for a set of units
AffymetrixCdfFile$fromFile

Defines an AffymetrixCdfFile object from a CDF file
extractFeatureSet.AffymetrixCelSet

Extracts CEL signals an in-memory FeatureSet object
doCRMAv2

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doRMA

Robust Multichip Analysis (RMA)
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
getChipType.SnpInformation

Gets the chip type of this genome information set
CrlmmParametersSet

The CrlmmParametersSet class
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
getAlias.GenericReporter

Gets the alias of the report
getAlias.Model

Gets the name alias for the model
fit.FirmaModel

Estimates the model parameters
ExonChipEffectFile

The ExonChipEffectFile class
fit.Model

Estimates the model parameters
getData.GenomeInformation

Gets all or a subset of the genome information data
findUnitsTodo.FirmaModel

Identifies non-fitted units
getData.SnpInformation

Gets all or a subset of the genome information data
getDataSet.Model

Gets the input data set for this model
getFirmaSet.FirmaModel

Gets the set of FIRMA results for this model
ExonChipEffectSet

The ExonChipEffectSet class
getHeader.AffymetrixCdfFile

Gets the header of the CDF file
GenericReporter

The GenericReporter class
getFitUnitGroupFunction.AffinePlm

Gets the low-level function that fits the PLM
doFIRMA

Finding Isoforms using Robust Multichip Analysis (FIRMA)
GenomeInformation

The GenomeInformation class
MatSmoothing

The MatSmoothing class
getHeader.AffymetrixCelFile

Gets the header of the CEL file
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
getOutputDataSet.TransformReport

Gets the transformed data set
findUnitsTodo.UnitModel

Identifies non-fitted units
getPath.Model

Gets the path of this model
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
getResiduals.QualityAssessmentModel

Calculates the residuals from a probe-level model
getAlleleProbePairs3.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
getFitUnitGroupFunction.AvgPlm

Gets the low-level function that fits the PLM
getFullName.TransformReport

Gets the full name of the output data set
getGenomeInformation.AffymetrixCdfFile

Gets genome information for this chip type
getHeader.CnagCfhFile

Gets the header of the CEL file
getAverageFile.AffymetrixCelSet

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set
MbeiCnPlm

The MbeiCnPlm class
getImage.AffymetrixCelFile

Creates an RGB Image object from a CEL file
ProbeLevelModel

The ProbeLevelModel class
getTags.GenericReporter

Gets the tags of the reporter
getTags.Model

Gets the tags of the output data set
fitQuantileNormFcn.AffymetrixCelFile

Fits quantile normalization functions for the arrays in the data set
getAlleleCellPairs.AffymetrixCdfFile

Gets the cell indices of allele pairs
getCdf.CnagCfhFile

Gets the CDF structure for this CEL file
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
GenomeInformation$fromCdf

Static method to define a genome information set from a CDF
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
getWeights.QualityAssessmentModel

Calculates the weights from the robust fit to a probe-level model
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
getXAM.ChipEffectFile

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
getCellIndices.ExonProbeAffinityFile

Retrieves tree list of cell indices for a set of units
ProbeLevelTransform

The ProbeLevelTransform class
getAlleleProbePairs.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
ResidualFile

The ResidualFile class
getCellIndices.FirmaFile

Retrieves tree list of cell indices for a set of units
SnpInformation$fromCdf

Static method to define a genome information set from a CDF
getAverageFile.CnagCfhSet

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CFH set
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
AromaChipTypeAnnotationFile$fromFile

Sets up an AromaChipTypeAnnotationFile
getCellIndices.ProbeAffinityFile

Retrieves tree list of cell indices for a set of units
ResidualSet

The ResidualSet class
getChipType.CnagCfhFile

Gets the chip type for this CEL file
getDataSet.AffymetrixCelSetReporter

Gets the data set
UnitModel

The UnitModel class
isPm.AffymetrixCdfFile

Checks which cells (probes) are PMs and not
getChipType.GenomeInformation

Gets the chip type of this genome information set
getCellIndices.ResidualFile

Retrieves tree list of cell indices for a set of units
process.DChipQuantileNormalization

Normalizes the data set
isResequenceChip.AffymetrixCdfFile

Static method to check if a CDF is for a resequencing (CustomSeq) chip
getFitUnitGroupFunction.ExonRmaPlm

Gets the low-level function that fits the Exon PLM
writeImage.AffymetrixCelFile

Writes a spatial image of the signals in the CEL file
CnChipEffectSet$importFromApt

Imports copy-number estimates from an APT summary file
process.MatSmoothing

Processes the data set
getChipEffectSet.AlleleSummation

Gets the set of chip effects for this model
plotBoxplotStats.list

Plots a (merged or non-merged) list of boxplot.stats() elements
UnitTypeScaleNormalization

The UnitTypeScaleNormalization class
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
getFullName.Model

Gets the full name of the output set
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
getDataSet.ArrayExplorer

Gets the data set
CnagCfhFile$fromFile

Defines an CnagCfhFile object from a CFH file
getCellIndices.ChipEffectFile

Retrieves tree list of cell indices for a set of units
getCellIndices.CnChipEffectFile

Retrieves tree list of cell indices for a set of units
pdInfo2Cdf

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type
process.OpticalBackgroundCorrection

Performs background correction
process.AbstractProbeSequenceNormalization

Normalizes the data set
verify.SnpInformation

Verifies the correctness of the underlying file
isSnpChip.AffymetrixCdfFile

Static method to check if a chip is a mapping (SNP) chip
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
process.FragmentEquivalentClassNormalization

Normalizes the data set
SingleArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
readRawData.AffymetrixCelFile

Gets all or a subset of the fields in a CEL file
process.UnitTypeScaleNormalization

Normalizes the data set
getFitUnitGroupFunction.FirmaModel

Static method to get the low-level function that fits the PLM
computeAffinities.AffymetrixCdfFile

Calculates probe affinities from sequence
getXAM.ChipEffectSet

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
getPath.TransformReport

Gets the path of the output data set
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
getCellIndices.UnitModel

Gets the cell indices unit by unit
getInputDataSet.TransformReport

Gets the source data set
getName.GenericReporter

Gets the name of the explorer
getCellIndices.WeightsFile

Retrieves tree list of cell indices for a set of units
setCdf.CnagCfhFile

Sets the CDF structure for this CEL file
getFitUnitGroupFunction.RmaPlm

Gets the low-level function that fits the PLM
getIntensities.AffymetrixCelSet

Gets cell intensities from a set of cells and a set of arrays
randomSeed

Sets and resets the .Random.seed in the global environment
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
getPositions.GenomeInformation

Gets the physical positions for a set of units
plotMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a scatter plot
convert.AffymetrixCdfFile

Converts a CDF into the same CDF but with another format
getFitUnitGroupFunction.HetLogAddPlm

Gets the low-level function that fits the PLM
process.FragmentLengthNormalization

Normalizes the data set
getTags.TransformReport

Gets the tags of the output data set
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
getFitUnitGroupFunction.MbeiPlm

Gets the low-level function that fits the PLM
plotMvsX.AffymetrixCelFile

Plots log-ratio versus another variable in a scatter plot
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
process.GcContentNormalization

Normalizes the data set
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
process.ScaleNormalization3

Normalizes the data set
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
MultiArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
setCdf.AffymetrixCelSet

Sets the CDF structure for this CEL set
getUnitNames.AffymetrixPgfFile

Gets the names of each unit
extractAffyBatch.AffymetrixCelSet

Extracts an in-memory AffyBatch object from the CEL set
plotDensity.AffymetrixCelFile

Plots the density of the probe signals on the array
process.AdditiveCovariatesNormalization

Normalizes the data set
readUnits.MultiArrayUnitModel

Reads data unit by unit
extractDataFrame.ParameterCelSet

Extract data as a data.frame for a set of arrays
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
getName.Model

Gets the name of the output data set
justRMA

Robust Multichip Analysis (RMA) reproducing the affy package
AffymetrixCdfFile$findByChipType

Locates a CDF file from its chip type
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
process.AllelicCrosstalkCalibration

Calibrates the data set
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
AffymetrixPgfFile$findByChipType

Locates a PGF file from its chip type
updateUnits.AffymetrixCelFile

Updates CEL data unit by unit
setAlias.Model

Sets the name alias for the model
fit.ProbeLevelModel

Estimates the model parameters
getRootPath.Model

Gets the root path of this model
process.ArrayExplorer

Generates image files, scripts and dynamic pages for the explorer
getSnpNames.AffymetrixCdfFile

Gets the names of the SNP units
fit.SingleArrayUnitModel

Estimates the model parameters
normalizeQuantile.AffymetrixCelFile

Normalizes the probe intensities to a target empirical distribution
getAM.ChipEffectSet

Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file
getAM.ChipEffectFile

Gets the log-intensities and log-ratios of chip effects for two arrays
getCdf.Model

Gets the CDF structure for this model
process.GenericReporter

Generates report
setArrays.ArrayExplorer

Sets the arrays
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
process.LimmaBackgroundCorrection

Performs background correction
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
getName.TransformReport

Gets the name of the output data set
getCellIndices.AffymetrixCdfFile

Gets the cell indices unit by unit
process.GcRmaBackgroundCorrection

Performs background correction
getCellIndices.SnpChipEffectFile

Retrieves tree list of cell indices for a set of units
getCellIndices.SnpProbeAffinityFile

Retrieves tree list of cell indices for a set of units
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
setAlias.GenericReporter

Sets the alias of the report
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
getChipType.AffymetrixCelFile

Gets the chip type for this CEL file
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
verify.GenomeInformation

Verifies the correctness of the underlying file
process.QuantileNormalization

Normalizes the data set
AffymetrixCelSet$importFromDChip

Imports dChip-exported CEL files
CnChipEffectSet$importFromDChip

Imports copy-number estimates from a dChip result file
getHeader.AffymetrixPgfFile

Gets the header of the PGF file
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
getHeader.AromaChipTypeAnnotationFile

Gets the header of the annotation file
process.ReseqCrosstalkCalibration

Calibrates the data set
plotDensity.AffymetrixCelSet

Plots the densities of all samples
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
process.MatNormalization

Normalizes the data set
process.ScaleNormalization

Normalizes the data set
getOutputDataSet.Transform

Gets the transformed data set
process.RmaBackgroundCorrection

Performs background correction
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
setTags.Model

Sets the tags to be appended
readUnits.SingleArrayUnitModel

Reads data unit by unit
process.BackgroundCorrection

Processes the data set
setRestructor.AffymetrixCdfFile

Specifies a function through which
process.ChipEffectGroupMerge

Normalizes the data set
readUnits.AffymetrixCelFile

Reads CEL data unit by unit
setupExampleData.AromaAffymetrix

Setups example data in the current directory
readUnits.CnagCfhFile

Reads CEL data unit by unit
smoothScatterMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a smooth scatter plot