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aroma.affymetrix (version 3.0.0)

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

608

Version

3.0.0

License

LGPL (>= 2.1)

Issues

9

Pull Requests

0

Stars

10

Forks

3

Maintainer

Henrik Bengtsson

Last Published

January 9th, 2016

Functions in aroma.affymetrix (3.0.0)

CnChipEffectSet

The CnChipEffectSet class
AvgSnpPlm

The AvgSnpPlm class
AffineCnPlm

The AffineCnPlm class
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
AffymetrixCelSet

The AffymetrixCelSet class
FragmentLengthNormalization

The FragmentLengthNormalization class
ChipEffectTransform

The ChipEffectTransform class
RmaSnpPlm

The RmaSnpPlm class
MbeiCnPlm

The MbeiCnPlm class
AffymetrixPgfFile

The AffymetrixPgfFile class
MultiArrayUnitModel

The MultiArrayUnitModel class
ArrayExplorer

The ArrayExplorer class
DChipQuantileNormalization

The DChipQuantileNormalization class
Non-documented objects

Non-documented objects
DChipCdfBinFile

The DChipCdfBinFile class
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
AffymetrixFileSet

The AffymetrixFileSet class
ChipEffectSet

The ChipEffectSet class
AffymetrixCnChpSet

The AffymetrixCnChpSet class
Model

The Model class
AffinePlm

The AffinePlm class
aroma.affymetrix-package

Package aroma.affymetrix
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
CnChipEffectFile

The CnChipEffectFile class
MatNormalization

The MatNormalization class
ReseqCrosstalkCalibration

The ReseqCrosstalkCalibration class
NormExpBackgroundCorrection

The NormExpBackgroundCorrection class
HetLogAddPlm

The HetLogAddPlm class
AvgPlm

The AvgPlm class
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
ExonChipEffectFile

The ExonChipEffectFile class
ChipEffectGroupMerge

The ChipEffectGroupMerge class
FirmaSet

The FirmaSet class
QualityAssessmentModel

The QualityAssessmentModel class
AlleleSummation

The AlleleSummation class
FirmaModel

The FirmaModel class
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
GenericReporter

The GenericReporter class
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
AffineSnpPlm

The AffineSnpPlm class
ChipEffectFile

The ChipEffectFile class
DChipDcpFile

The DChipDcpFile class
ResidualSet

The ResidualSet class
BasePositionNormalization

The BasePositionNormalization class
DChipSnpInformation

The DChipSnpInformation class
AffymetrixFile

The abstract AffymetrixFile class
GcContentNormalization2

The GcContentNormalization2 class
ProbeLevelTransform3

The ProbeLevelTransform3 class
FirmaFile

The FirmaFile class
ProbeLevelModel

The ProbeLevelModel class
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
MatSmoothing

The MatSmoothing class
TransformReport

The TransformReport class
AromaChipTypeAnnotationFile

The AromaChipTypeAnnotationFile class
CnProbeAffinityFile

The CnProbeAffinityFile class
ExonRmaPlm

The ExonRmaPlm class
QualityAssessmentFile

The QualityAssessmentFile class
AffymetrixCelFile

The AffymetrixCelFile class
GenomeInformation$byChipType

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

The DChipDcpSet class
GenomeInformation

The GenomeInformation class
AffymetrixFileSet$byPath

Defines an AffymetrixFileSet object by searching for Affymetrix files
ChipEffectFile$fromDataFile

Retrive an existing CEL file, or create from CDF template if missing
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
ParameterCelSet

The ParameterCelSet class
ProbeAffinityFile

The ProbeAffinityFile class
ExonChipEffectSet

The ExonChipEffectSet class
ProbeLevelTransform

The ProbeLevelTransform class
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
CnagCfhSet

The CnagCfhSet class
getAM.ChipEffectSet

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

The DChipGenomeInformation class
convert.AffymetrixCdfFile

Converts a CDF into the same CDF but with another format
BaseCountNormalization

The BaseCountNormalization class
QualityAssessmentSet

The QualityAssessmentSet class
doCRMAv1

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

The ExonProbeAffinityFile class
ScaleNormalization

The ScaleNormalization class
RmaCnPlm

The RmaCnPlm class
LinearModelProbeSequenceNormalization

The LinearModelProbeSequenceNormalization class
AvgCnPlm

The AvgCnPlm class
ParameterCelFile

The ParameterCelFile class
SnpPlm

The SnpPlm interface class
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
AffymetrixCdfFile

The AffymetrixCdfFile class
RmaBackgroundCorrection

The RmaBackgroundCorrection class
CrlmmParametersFile

The CrlmmParametersFile class
SnpInformation

The SnpInformation class
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
CnagCfhFile

The CnagCfhFile class
BackgroundCorrection

The BackgroundCorrection class
CrlmmParametersSet

The CrlmmParametersSet class
fit.Model

Estimates the model parameters
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
MbeiPlm

The MbeiPlm class
QuantileNormalization

The QuantileNormalization class
WeightsFile

The WeightsFile class
SnpChipEffectFile

The SnpChipEffectFile class
CnPlm

The CnPlm class
CnagCfhFile$fromFile

Defines an CnagCfhFile object from a CFH file
getAlias.GenericReporter

Gets the alias of the report
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
getChipType.AffymetrixCelFile

Gets the chip type for this CEL file
getAlleleProbePairs.AffymetrixCdfFile

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

The SmoothMultiarrayModel class
as.AffymetrixCnChpSet.AffymetrixCnChpSet

Coerce an object to an AffymetrixCnChpSet object
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
HetLogAddCnPlm

The HetLogAddCnPlm class
bpmapCluster2Cdf

Creates a CDF from tiling-array BPMAP file
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
SnpProbeAffinityFile

The SnpProbeAffinityFile class
GcContentNormalization

The GcContentNormalization class
AromaChipTypeAnnotationFile$byChipType

Defines an AromaChipTypeAnnotationFile object by chip type
getName.GenericReporter

Gets the name of the explorer
UnitModel

The UnitModel class
ScaleNormalization3

The ScaleNormalization3 class
convertUnits.AffymetrixCdfFile

Gets and validates unit indices
byChipType.SnpInformation

Static method to define a genome information set by chip type
extractMatrix.AffymetrixCelSet

Extract data as a matrix for a set of arrays
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
SmoothRmaModel

The SmoothRmaModel class
getCdf.CnagCfhFile

Gets the CDF structure for this CEL file
SnpChipEffectSet

The SnpChipEffectSet class
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
AffymetrixCdfFile$findByChipType

Locates a CDF file from its chip type
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
AffymetrixCelFile$allocateFromCdf

Creates an empty CEL file from a template CDF
WeightsSet

The WeightsSet class
UnitTypeScaleNormalization

The UnitTypeScaleNormalization class
as.AffymetrixCelSet.AffymetrixCelSet

Coerce an object to an AffymetrixCelSet object
extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
AffymetrixPgfFile$findByChipType

Locates a PGF file from its chip type
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
getChipEffectSet.AlleleSummation

Gets the set of chip effects for this model
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
compare.AffymetrixCdfFile

Checks if two AffymetrixCdfFile objects are equal
getIntensities.AffymetrixCelSet

Gets cell intensities from a set of cells and a set of arrays
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
getAverageFile.AffymetrixCelSet

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

Extract data as a data.frame for a set of arrays
fit.FirmaModel

Estimates the model parameters
process.ChipEffectGroupMerge

Normalizes the data set
HetLogAddSnpPlm

The HetLogAddSnpPlm class
as.character.AffymetrixCelSet

Returns a short string describing the Affymetrix CEL set
getTags.Model

Gets the tags of the output data set
SpatialReporter

The SpatialReporter class
smoothScatterMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a smooth scatter plot
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
process.LimmaBackgroundCorrection

Performs background correction
getCellIndices.FirmaFile

Retrieves tree list of cell indices for a set of units
as.character.AffymetrixCnChpSet

Returns a short string describing the set
MultiArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
AffymetrixCdfFile$fromFile

Defines an AffymetrixCdfFile object from a CDF file
randomSeed

Sets and resets the .Random.seed in the global environment
getFitUnitGroupFunction.AffinePlm

Gets the low-level function that fits the PLM
getAlleleProbePairs3.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
getFullName.Model

Gets the full name of the output set
AffymetrixPgfFile$fromFile

Defines an AffymetrixPgfFile object from a PGF file
byChipType.DChipSnpInformation

Defines a DChipSnpInformation object by chip type
getCdf.Model

Gets the CDF structure for this model
SingleArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
AromaUnitTabularBinaryFile$allocateFromCdf

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
GenomeInformation$fromCdf

Static method to define a genome information set from a CDF
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
fit.ProbeLevelModel

Estimates the model parameters
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
getCellIndices.SnpProbeAffinityFile

Retrieves tree list of cell indices for a set of units
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
AffymetrixCelFile$fromFile

Defines an AffymetrixCelFile object from a CEL file
AromaChipTypeAnnotationFile$fromFile

Sets up an AromaChipTypeAnnotationFile
extractAffyBatch.AffymetrixCelSet

Extracts an in-memory AffyBatch object from the CEL set
getCellIndices.ResidualFile

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

Creates a unique-cell version of the CDF
getAM.ChipEffectFile

Gets the log-intensities and log-ratios of chip effects for two arrays
getHeader.AromaChipTypeAnnotationFile

Gets the header of the annotation file
getCellIndices.CnProbeAffinityFile

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

Retrieves tree list of cell indices for a set of units
doCRMAv2

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

Calculates probe affinities from sequence
doRMA

Robust Multichip Analysis (RMA)
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
getCellIndices.UnitModel

Gets the cell indices unit by unit
getCellIndices.ChipEffectFile

Retrieves tree list of cell indices for a set of units
getXAM.ChipEffectFile

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

Calculates the weights from the robust fit to a probe-level model
extractFeatureSet.AffymetrixCelSet

Extracts CEL signals an in-memory FeatureSet object
doGCRMA

Robust Multichip Analysis (GCRMA)
fit.SingleArrayUnitModel

Estimates the model parameters
getAverageFile.CnagCfhSet

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

Gets the set of FIRMA results for this model
getCellIndices.ExonProbeAffinityFile

Retrieves tree list of cell indices for a set of units
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
getOutputDataSet.TransformReport

Gets the transformed data set
getFitUnitGroupFunction.RmaPlm

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

Gets the name of the output data set
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
RmaPlm

The RmaPlm class
process.ScaleNormalization3

Normalizes the data set
getAlias.Model

Gets the name alias for the model
setAlias.Model

Sets the name alias for the model
plotDensity.AffymetrixCelFile

Plots the density of the probe signals on the array
getName.Model

Gets the name of the output data set
setTags.Model

Sets the tags to be appended
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
getFitUnitGroupFunction.MbeiPlm

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

Gets the CDF structure for this CEL set
getAlleleCellPairs.AffymetrixCdfFile

Gets the cell indices of allele pairs
getPath.Model

Gets the path of this model
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
getChipType.CnagCfhFile

Gets the chip type for this CEL file
process.OpticalBackgroundCorrection

Performs background correction
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
getFitUnitGroupFunction.AvgPlm

Gets the low-level function that fits the PLM
setRestructor.AffymetrixCdfFile

Specifies a function through which
readRawData.AffymetrixCelFile

Gets all or a subset of the fields in a CEL file
doFIRMA

Finding Isoforms using Robust Multichip Analysis (FIRMA)
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
process.UnitTypeScaleNormalization

Normalizes the data set
process.DChipQuantileNormalization

Normalizes the data set
getDataSet.Model

Gets the input data set for this model
process.BackgroundCorrection

Processes the data set
getHeader.AffymetrixCelFile

Gets the header of the CEL file
getOutputDataSet.Transform

Gets the transformed data set
getData.GenomeInformation

Gets all or a subset of the genome information data
getResiduals.QualityAssessmentModel

Calculates the residuals from a probe-level model
getCellIndices.SnpChipEffectFile

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

Checks which cells (probes) are PMs and not
readUnits.CnagCfhFile

Reads CEL data unit by unit
plotMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a scatter plot
getFitUnitGroupFunction.ExonRmaPlm

Gets the low-level function that fits the Exon PLM
getData.SnpInformation

Gets all or a subset of the genome information data
getFullName.TransformReport

Gets the full name of the output data set
getRootPath.Model

Gets the root path of this model
getInputDataSet.TransformReport

Gets the source data set
getCellIndices.WeightsFile

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

The LimmaBackgroundCorrection class
findUnitsTodo.UnitModel

Identifies non-fitted units
process.MatNormalization

Normalizes the data set
process.FragmentEquivalentClassNormalization

Normalizes the data set
verify.SnpInformation

Verifies the correctness of the underlying file
process.GcRmaBackgroundCorrection

Performs background correction
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
getHeader.AffymetrixCdfFile

Gets the header of the CDF file
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
process.AdditiveCovariatesNormalization

Normalizes the data set
getImage.AffymetrixCelFile

Creates an RGB Image object from a CEL file
nbrOfArrays.AffymetrixCelSet

Gets the number of arrays in the file set
AffymetrixCelFile$clearData

Clears all or a subset of the fields in a CEL file
process.AllelicCrosstalkCalibration

Calibrates the data set
getChipType.GenomeInformation

Gets the chip type of this genome information set
process.FragmentLengthNormalization

Normalizes the data set
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
getFitUnitGroupFunction.HetLogAddPlm

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

Gets the tags of the output data set
getSnpNames.AffymetrixCdfFile

Gets the names of the SNP units
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
getHeader.CnagCfhFile

Gets the header of the CEL file
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
getPositions.GenomeInformation

Gets the physical positions for a set of units
getChipType.SnpInformation

Gets the chip type of this genome information set
getDataSet.ArrayExplorer

Gets the data set
getXAM.ChipEffectSet

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

Updates CEL data unit by unit
pdInfo2Cdf

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxillary CEL file for the same chip type
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
getUnitNames.AffymetrixPgfFile

Gets the names of each unit
CnChipEffectSet$importFromDChip

Imports copy-number estimates from a dChip result file
AffymetrixCelSet$importFromDChip

Imports dChip-exported CEL files
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
isResequenceChip.AffymetrixCdfFile

Static method to check if a CDF is for a resequencing (CustomSeq) chip
process.GcContentNormalization

Normalizes the data set
process.MatSmoothing

Processes the data set
process.ArrayExplorer

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

Normalizes the data set
isSnpChip.AffymetrixCdfFile

Static method to check if a chip is a mapping (SNP) chip
verify.GenomeInformation

Verifies the correctness of the underlying file
setAlias.GenericReporter

Sets the alias of the report
process.GenericReporter

Generates report
readUnits.SingleArrayUnitModel

Reads data unit by unit
setCdf.CnagCfhFile

Sets the CDF structure for this CEL file
setCdf.AffymetrixCelSet

Sets the CDF structure for this CEL set
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
plotMvsX.AffymetrixCelFile

Plots log-ratio versus another variable in a scatter plot
plotBoxplotStats.list

Plots a (merged or non-merged) list of boxplot.stats() elements
CnChipEffectSet$importFromApt

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

Calibrates the data set
process.QuantileNormalization

Normalizes the data set
plotDensity.AffymetrixCelSet

Plots the densities of all samples
writeImage.AffymetrixCelFile

Writes a spatial image of the signals in the CEL file
readUnits.MultiArrayUnitModel

Reads data unit by unit
setArrays.ArrayExplorer

Sets the arrays
setupExampleData

Setups example data in the current directory
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
setupExampleData.AromaAffymetrix

Setups example data in the current directory
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
justRMA

Robust Multichip Analysis (RMA) reproducing the affy package
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
ResidualFile

The ResidualFile class
UgpGenomeInformation

The UgpGenomeInformation class
findUnitsTodo.FirmaModel

Identifies non-fitted units
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
SnpInformation$fromCdf

Static method to define a genome information set from a CDF
getCellIndices.ExonChipEffectFile

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

Gets the cell indices unit by unit
getCellIndices.CnChipEffectFile

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

Gets genome information for this chip type
getPath.TransformReport

Gets the path of the output data set
getTags.GenericReporter

Gets the tags of the reporter
normalizeQuantile.AffymetrixCelFile

Normalizes the probe intensities to a target empirical distribution
MbeiSnpPlm

The MbeiSnpPlm class
SingleArrayUnitModel

The SingleArrayUnitModel class
UgpGenomeInformation$byChipType

Defines a UgpGenomeInformation object by chip type
fitQuantileNormFcn.AffymetrixCelFile

Fits quantile normalization functions for the arrays in the data set
getDataSet.AffymetrixCelSetReporter

Gets the data set
getHeader.AffymetrixPgfFile

Gets the header of the PGF file
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
process.RmaBackgroundCorrection

Performs background correction
process.ScaleNormalization

Normalizes the data set
readUnits.AffymetrixCelFile

Reads CEL data unit by unit
getFitUnitGroupFunction.FirmaModel

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