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aroma.affymetrix (version 2.10.0)

Analysis of large Affymetrix microarray data sets

Description

This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the diskspace that limits the number of arrays that can be analyzed. To install, do: source("http://www.aroma-project.org/hbLite.R"); hbInstall("aroma.affymetrix").

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Version

Install

install.packages('aroma.affymetrix')

Monthly Downloads

669

Version

2.10.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

August 6th, 2013

Functions in aroma.affymetrix (2.10.0)

GcContentNormalization

The GcContentNormalization class
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
CnChipEffectFile

The CnChipEffectFile class
FirmaModel

The FirmaModel class
MbeiSnpPlm

The MbeiSnpPlm class
MbeiPlm

The MbeiPlm class
AffymetrixCnChpSet

The AffymetrixCnChpSet class
AffymetrixCdfFile

The AffymetrixCdfFile class
HetLogAddPlm

The HetLogAddPlm class
ProbeLevelModel

The ProbeLevelModel class
UnitModel

The UnitModel class
ArrayExplorer

The ArrayExplorer class
RmaPlm

The RmaPlm class
FragmentLengthNormalization

The FragmentLengthNormalization class
AffineCnPlm

The AffineCnPlm class
ProbeAffinityFile

The ProbeAffinityFile class
ParameterCelFile

The ParameterCelFile class
CrlmmParametersSet

The CrlmmParametersSet class
ChipEffectGroupMerge

The ChipEffectGroupMerge class
QualityAssessmentSet

The QualityAssessmentSet class
SnpProbeAffinityFile

The SnpProbeAffinityFile class
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
DChipQuantileNormalization

The DChipQuantileNormalization class
FirmaFile

The FirmaFile class
FirmaSet

The FirmaSet class
WeightsSet

The WeightsSet class
ExonChipEffectFile

The ExonChipEffectFile class
AffinePlm

The AffinePlm class
MatNormalization

The MatNormalization class
BasePositionNormalization

The BasePositionNormalization class
QualityAssessmentFile

The QualityAssessmentFile class
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
AffymetrixFileSet$byPath

Defines an AffymetrixFileSet object by searching for Affymetrix files
CnChipEffectSet

The CnChipEffectSet class
BaseCountNormalization

The BaseCountNormalization class
DChipDcpSet

The DChipDcpSet class
Model

The Model class
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
DChipSnpInformation

The DChipSnpInformation class
AvgPlm

The AvgPlm class
aroma.affymetrix-package

Package aroma.affymetrix
ExonChipEffectSet

The ExonChipEffectSet class
DChipCdfBinFile

The DChipCdfBinFile class
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
GenericReporter

The GenericReporter class
AvgSnpPlm

The AvgSnpPlm class
DChipGenomeInformation

The DChipGenomeInformation class
ChipEffectFile

The ChipEffectFile class
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
doRMA

Robust Multichip Analysis (RMA)
bgAdjustGcrma.AffymetrixCelFile

Applies probe sequence based background correction to a CEL file
bgAdjustGcrma.AffymetrixCelSet

Applies probe sequence based background correction to a set of CEL files
doGCRMA

Robust Multichip Analysis (GCRMA)
SnpInformation

The SnpInformation class
ChipEffectTransform

The ChipEffectTransform class
CnPlm

The CnPlm class
AromaChipTypeAnnotationFile$byChipType

Defines an AromaChipTypeAnnotationFile object by chip type
SpatialReporter

The SpatialReporter class
AffymetrixFile

The abstract AffymetrixFile class
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
TransformReport

The TransformReport class
ProbeLevelTransform

The ProbeLevelTransform 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
HetLogAddSnpPlm

The HetLogAddSnpPlm class
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
getCellIndices.WeightsFile

Retrieves tree list of cell indices for a set of units
getAlleleProbePairs3.AffymetrixCdfFile

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

The MbeiCnPlm class
AvgCnPlm

The AvgCnPlm class
ExonProbeAffinityFile

The ExonProbeAffinityFile class
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
SnpChipEffectFile

The SnpChipEffectFile class
SnpPlm

The SnpPlm interface class
RmaCnPlm

The RmaCnPlm class
DChipDcpFile

The DChipDcpFile class
extractDataFrame.ParameterCelSet

Extract data as a data.frame for a set of arrays
AlleleSummation

The AlleleSummation class
extractMatrix.AffymetrixCelSet

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

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

Gets the header of the CEL file
RmaSnpPlm

The RmaSnpPlm class
LinearModelProbeSequenceNormalization

The LinearModelProbeSequenceNormalization class
AffymetrixPgfFile

The AffymetrixPgfFile class
getWeights.QualityAssessmentModel

Calculates the weights from the robust fit to a probe-level model
SingleArrayUnitModel

The SingleArrayUnitModel class
doFIRMA

Finding Isoforms using Robust Multichip Analysis (FIRMA)
CnagCfhSet

The CnagCfhSet class
getData.GenomeInformation

Gets all or a subset of the genome information data
CnagCfhFile

The CnagCfhFile class
AffineSnpPlm

The AffineSnpPlm class
MultiArrayUnitModel

The MultiArrayUnitModel class
ScaleNormalization

The ScaleNormalization class
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
getXAM.ChipEffectSet

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
BackgroundCorrection

The BackgroundCorrection class
AffymetrixFileSet

The AffymetrixFileSet class
CnProbeAffinityFile

The CnProbeAffinityFile class
GcContentNormalization2

The GcContentNormalization2 class
ParameterCelSet

The ParameterCelSet class
AffymetrixCelSet

The AffymetrixCelSet class
getXAM.ChipEffectFile

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

The AffymetrixCelFile class
ProbeLevelTransform3

The ProbeLevelTransform3 class
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
GenomeInformation$byChipType

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

The ResidualFile class
computeAffinities.AffymetrixCdfFile

Calculates probe affinities from sequence
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
GenomeInformation

The GenomeInformation class
AffymetrixCdfFile$findByChipType

Locates a CDF file from its chip type
CrlmmParametersFile

The CrlmmParametersFile class
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
ReseqCrosstalkCalibration

The ReseqCrosstalkCalibration class
extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
getCellIndices.UnitModel

Gets the cell indices unit by unit
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
getAlleleCellPairs.AffymetrixCdfFile

Gets the cell indices of allele pairs
process.GcRmaBackgroundCorrection

Performs background correction
getTags.GenericReporter

Gets the tags of the reporter
AromaChipTypeAnnotationFile$fromFile

Sets up an AromaChipTypeAnnotationFile
getCellIndices.AffymetrixCdfFile

Gets the cell indices unit by unit
getCellIndices.CnProbeAffinityFile

Retrieves tree list of cell indices for a set of units
getCdf.AffymetrixCelSet

Gets the CDF structure for this CEL set
SmoothMultiarrayModel

The SmoothMultiarrayModel class
getAlias.GenericReporter

Gets the alias of the report
QualityAssessmentModel

The QualityAssessmentModel class
getCellIndices.ChipEffectFile

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

Coerce an object to an AffymetrixCelSet object
SnpInformation$fromCdf

Static method to define a genome information set from a CDF
AffymetrixPgfFile$fromFile

Defines an AffymetrixPgfFile object from a PGF file
UgpGenomeInformation$byChipType

Defines a UgpGenomeInformation object by chip type
getChipType.AffymetrixCelFile

Gets the chip type for this CEL file
AffymetrixCelFile$allocateFromCdf

Creates an empty CEL file from a template CDF
process.MatNormalization

Normalizes the data set
getCellIndices.ExonProbeAffinityFile

Retrieves tree list of cell indices for a set of units
getFitUnitGroupFunction.HetLogAddPlm

Gets the low-level function that fits the PLM
getDataSet.AffymetrixCelSetReporter

Gets the data set
getCellIndices.ResidualFile

Retrieves tree list of cell indices for a set of units
AffymetrixCelFile$clearData

Clears all or a subset of the fields in a CEL file
SmoothRmaModel

The SmoothRmaModel class
AffymetrixCdfFile$fromFile

Defines an AffymetrixCdfFile object from a CDF file
AffymetrixCelSet$importFromDChip

Imports dChip-exported CEL files
getAlias.Model

Gets the name alias for the model
fit.ProbeLevelModel

Estimates the model parameters
getChipType.GenomeInformation

Gets the chip type of this genome information set
getChipEffectSet.AlleleSummation

Gets the set of chip effects for this model
process.DChipQuantileNormalization

Normalizes the data set
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
plotDensity.AffymetrixCelFile

Plots the density of the probe signals on the array
updateUnits.AffymetrixCelFile

Updates CEL data unit by unit
getPath.Model

Gets the path of this model
getAM.ChipEffectSet

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

Estimates the model parameters
as.AffymetrixCnChpSet.AffymetrixCnChpSet

Coerce an object to an AffymetrixCnChpSet object
getAlleleProbePairs.AffymetrixCdfFile

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

The UnitTypeScaleNormalization class
compare.AffymetrixCdfFile

Checks if two AffymetrixCdfFile objects are equal
getTags.TransformReport

Gets the tags of the output data set
SnpChipEffectSet

The SnpChipEffectSet class
CnagCfhFile$fromFile

Defines an CnagCfhFile object from a CFH file
getFitUnitGroupFunction.AffinePlm

Gets the low-level function that fits the PLM
findUnitsTodo.FirmaModel

Identifies non-fitted units
setAlias.GenericReporter

Sets the alias of the report
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
getUnitNames.AffymetrixPgfFile

Gets the names of each unit
getFullName.Model

Gets the full name of the output set
MatSmoothing

The MatSmoothing class
as.character.AffymetrixCnChpSet

Returns a short string describing the set
Non-documented objects

Non-documented objects
bgAdjustRma.AffymetrixCelFile

Applies normExp background correction to a CEL file
getOutputDataSet.TransformReport

Gets the transformed data set
pdInfo2Cdf

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

The ChipEffectSet class
getSnpNames.AffymetrixCdfFile

Gets the names of the SNP units
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
byChipType.DChipSnpInformation

Defines a DChipSnpInformation object by chip type
getHeader.CnagCfhFile

Gets the header of the CEL file
getChipType.SnpInformation

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

Processes the data set
convert.AffymetrixCdfFile

Converts a CDF into the same CDF but with another format
getResiduals.QualityAssessmentModel

Calculates the residuals from a probe-level model
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
as.character.AffymetrixCelSet

Returns a short string describing the Affymetrix CEL set
getCellIndices.ExonChipEffectFile

Retrieves tree list of cell indices for a set of units
AromaUnitTabularBinaryFile$allocateFromCdf

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
CnChipEffectSet$importFromDChip

Imports copy-number estimates from a dChip result file
getData.SnpInformation

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

Gets the input data set for this model
getIntensities.AffymetrixCelSet

Gets cell intensities from a set of cells and a set of arrays
process.ScaleNormalization

Normalizes the data set
fit.Model

Estimates the model parameters
HetLogAddCnPlm

The HetLogAddCnPlm class
RmaBackgroundCorrection

The RmaBackgroundCorrection class
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
bgAdjustOptical.AffymetrixCelFile

Applies optical background correction to a CEL file
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
isResequenceChip.AffymetrixCdfFile

Static method to check if a CDF is for a resequencing (CustomSeq) chip
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
getHeader.AromaChipTypeAnnotationFile

Gets the header of the annotation file
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
nbrOfArrays.AffymetrixCelSet

Gets the number of arrays in the file set
isSnpChip.AffymetrixCdfFile

Static method to check if a chip is a mapping (SNP) chip
getCellIndices.FirmaFile

Retrieves tree list of cell indices for a set of units
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
getOutputDataSet.Transform

Gets the transformed data set
process.LimmaBackgroundCorrection

Performs background correction
plotDensity.AffymetrixCelSet

Plots the densities of all samples
readUnits.MultiArrayUnitModel

Reads data unit by unit
setArrays.ArrayExplorer

Sets the arrays
AffymetrixCelFile$fromFile

Defines an AffymetrixCelFile object from a CEL file
ChipEffectFile$fromDataFile

Retrive an existing CEL file, or create from CDF template if missing
process.FragmentLengthNormalization

Normalizes the data set
process.UnitTypeScaleNormalization

Normalizes the data set
getPositions.GenomeInformation

Gets the physical positions for a set of units
GenomeInformation$fromCdf

Static method to define a genome information set from a CDF
process.RmaBackgroundCorrection

Performs background correction
process.MatSmoothing

Processes the data set
getName.Model

Gets the name of the output data set
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
getName.TransformReport

Gets the name of the output data set
getCdf.CnagCfhFile

Gets the CDF structure for this CEL file
getGenomeInformation.AffymetrixCdfFile

Gets genome information for this chip type
findUnitsTodo.UnitModel

Identifies non-fitted units
fitQuantileNormFcn.AffymetrixCelFile

Fits quantile normalization functions for the arrays in the data set
getFitUnitGroupFunction.RmaPlm

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

Sets the CDF structure for this CEL set
CnChipEffectSet$importFromApt

Imports copy-number estimates from an APT summary file
writeImage.AffymetrixCelFile

Writes a spatial image of the signals in the CEL file
getAM.ChipEffectFile

Gets the log-intensities and log-ratios of chip effects for two arrays
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
nbrOfArrays.AffymetrixCnChpSet

Gets the number of arrays in the file set
doCRMAv2

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

Generates report
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
process.ScaleNormalization3

Normalizes the data set
getChipType.CnagCfhFile

Gets the chip type for this CEL file
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
setRestructor.AffymetrixCdfFile

Specifies a function through which
setTags.Model

Sets the tags to be appended
doCRMAv1

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

Verifies the correctness of the underlying file
process.ArrayExplorer

Generates image files, scripts and dynamic pages for the explorer
getCellIndices.CnChipEffectFile

Retrieves tree list of cell indices for a set of units
readUnits.AffymetrixCelFile

Reads CEL data unit by unit
setCdf.CnagCfhFile

Sets the CDF structure for this CEL file
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
getFitUnitGroupFunction.MbeiPlm

Gets the low-level function that fits the PLM
nbrOfArrays.CnagCfhSet

Gets the number of arrays in the file set
readUnits.CnagCfhFile

Reads CEL data unit by unit
getPath.TransformReport

Gets the path of the output data set
getTags.Model

Gets the tags of the output data set
process.ReseqCrosstalkCalibration

Calibrates the data set
process.OpticalBackgroundCorrection

Performs background correction
plotMvsX.AffymetrixCelFile

Plots log-ratio versus another variable in a scatter plot
setAlias.Model

Sets the name alias for the model
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
getCellIndices.ProbeAffinityFile

Retrieves tree list of cell indices for a set of units
MultiArrayUnitModel$getFitUnitGroupFunction

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

Gets the header of the CDF file
nbrOfArrays.DChipDcpSet

Gets the number of arrays in the file set
process.AbstractProbeSequenceNormalization

Normalizes the data set
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
getCdf.Model

Gets the CDF structure for this model
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
getFitUnitGroupFunction.ExonRmaPlm

Gets the low-level function that fits the Exon PLM
getHeader.AffymetrixPgfFile

Gets the header of the PGF file
readUnits.SingleArrayUnitModel

Reads data unit by unit
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
smoothScatterMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a smooth scatter plot
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
getFitUnitGroupFunction.AvgPlm

Gets the low-level function that fits the PLM
plotBoxplotStats.list

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

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

Normalizes the data set
getFitUnitGroupFunction.FirmaModel

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

Verifies the correctness of the underlying file
isPm.AffymetrixCdfFile

Checks which cells (probes) are PMs and not
getFullName.TransformReport

Gets the full name of the output data set
process.AllelicCrosstalkCalibration

Calibrates the data set
normalizeQuantile.AffymetrixCelFile

Normalizes the probe intensities to a target empirical distribution
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
AromaChipTypeAnnotationFile

The AromaChipTypeAnnotationFile class
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
NormExpBackgroundCorrection

The NormExpBackgroundCorrection class
ExonRmaPlm

The ExonRmaPlm class
QuantileNormalization

The QuantileNormalization class
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
createUniqueCdf.AffymetrixCdfFile

Creates a unique-cell version of the CDF
getAverageFile.AffymetrixCelSet

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

Retrieves tree list of cell indices for a set of units
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
getCellIndices.SnpProbeAffinityFile

Retrieves tree list of cell indices for a set of units
getFirmaSet.FirmaModel

Gets the set of FIRMA results for this model
SingleArrayUnitModel$getFitUnitGroupFunction

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

Creates an RGB Image object from a CEL file
getName.GenericReporter

Gets the name of the explorer
getInputDataSet.TransformReport

Gets the source data set
getRootPath.Model

Gets the root path of this model
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
process.AdditiveCovariatesNormalization

Normalizes the data set
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
process.FragmentEquivalentClassNormalization

Normalizes the data set
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
LimmaBackgroundCorrection

The LimmaBackgroundCorrection class
ResidualSet

The ResidualSet class
UgpGenomeInformation

The UgpGenomeInformation class
WeightsFile

The WeightsFile class
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
AffymetrixPgfFile$findByChipType

Locates a PGF file from its chip type
fit.SingleArrayUnitModel

Estimates the model parameters
extractFeatureSet.AffymetrixCelSet

Extracts CEL signals an in-memory FeatureSet object
bpmapCluster2Cdf

Creates a CDF from tiling-array BPMAP file
getDataSet.ArrayExplorer

Gets the data set
plotMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a scatter plot
process.QuantileNormalization

Normalizes the data set
readRawData.AffymetrixCelFile

Gets all or a subset of the fields in a CEL file
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
process.GcContentNormalization

Normalizes the data set