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aroma.affymetrix (version 2.5.0)

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

608

Version

2.5.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

March 26th, 2012

Functions in aroma.affymetrix (2.5.0)

extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
allocateFromCdf.AffymetrixCelFile

Creates an empty CEL file from a template CDF
ScaleNormalization3

The ScaleNormalization3 class
AvgCnPlm

The AvgCnPlm class
AffinePlm

The AffinePlm class
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
ArrayExplorer

The ArrayExplorer class
SmoothRmaModel

The SmoothRmaModel class
as.AffymetrixCelSet.AffymetrixCelSet

Coerce an object to an AffymetrixCelSet object
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
WeightsFile

The WeightsFile class
ProbeLevelTransform

The ProbeLevelTransform class
CnagCfhFile

The CnagCfhFile class
pdInfo2Cdf

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

Defines a UgpGenomeInformation object by chip type
BasePositionNormalization

The BasePositionNormalization class
AffymetrixFile

The abstract AffymetrixFile class
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
DChipDcpSet

The DChipDcpSet class
verify.GenomeInformation

Verifies the correctness of the underlying file
byPath.AffymetrixFileSet

Defines an AffymetrixFileSet object by searching for Affymetrix files
CnProbeAffinityFile

The CnProbeAffinityFile class
fromCdf.GenomeInformation

Static method to define a genome information set from a CDF
AffymetrixCdfFile

The AffymetrixCdfFile class
findUnitsTodo.FirmaModel

Identifies non-fitted units
fromFile.AffymetrixCelFile

Defines an AffymetrixCelFile object from a CEL file
AffymetrixFileSet

The AffymetrixFileSet class
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
CnagCfhSet

The CnagCfhSet class
AvgPlm

The AvgPlm class
compare.AffymetrixCdfFile

Checks if two AffymetrixCdfFile objects are equal
FirmaModel

The FirmaModel class
HetLogAddCnPlm

The HetLogAddCnPlm class
getIntensities.AffymetrixCelSet

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

The DChipQuantileNormalization class
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
BaseCountNormalization

The BaseCountNormalization class
Model

The Model class
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
ExonProbeAffinityFile

The ExonProbeAffinityFile class
SnpChipEffectFile

The SnpChipEffectFile class
DChipSnpInformation

The DChipSnpInformation class
GenericReporter

The GenericReporter class
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
HetLogAddSnpPlm

The HetLogAddSnpPlm class
ResidualFile

The ResidualFile class
SnpChipEffectSet

The SnpChipEffectSet class
getPath.TransformReport

Gets the path of the output data set
getData.GenomeInformation

Gets all or a subset of the genome information data
getHeader.AffymetrixCdfFile

Gets the header of the CDF file
isResequenceChip.AffymetrixCdfFile

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

Applies optical background correction to a set of CEL files
ChipEffectGroupMerge

The ChipEffectGroupMerge class
MbeiSnpPlm

The MbeiSnpPlm class
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
LimmaBackgroundCorrection

The LimmaBackgroundCorrection class
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
AffymetrixCelSet

The AffymetrixCelSet class
Non-documented objects

Non-documented objects
ChipEffectSet

The ChipEffectSet class
AffymetrixCelFile

The AffymetrixCelFile class
UgpGenomeInformation

The UgpGenomeInformation class
SnpInformation

The SnpInformation class
ExonChipEffectFile

The ExonChipEffectFile class
RmaBackgroundCorrection

The RmaBackgroundCorrection class
RmaCnPlm

The RmaCnPlm class
fit.Model

Estimates the model parameters
nbrOfArrays.AffymetrixCnChpSet

Gets the number of arrays in the file set
FirmaSet

The FirmaSet class
ProbeLevelModel

The ProbeLevelModel class
getInputDataSet.TransformReport

Gets the source data set
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
AlleleSummation

The AlleleSummation class
FirmaFile

The FirmaFile class
fromFile.AffymetrixCdfFile

Defines an AffymetrixCdfFile object from a CDF file
getAM.ChipEffectSet

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

The AromaChipTypeAnnotationFile class
ProbeAffinityFile

The ProbeAffinityFile class
MatSmoothing

The MatSmoothing class
getFitUnitGroupFunction.HetLogAddPlm

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

Gets the transformed data set
findUnitsTodo.UnitModel

Identifies non-fitted units
plotBoxplotStats.list

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

The ParameterCelFile class
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
UnitTypeScaleNormalization

The UnitTypeScaleNormalization class
CrlmmParametersFile

The CrlmmParametersFile class
ParameterCelSet

The ParameterCelSet class
RmaSnpPlm

The RmaSnpPlm class
as.character.AffymetrixCnChpSet

Returns a short string describing the set
getFullName.Model

Gets the full name of the output set
ProbeLevelTransform3

The ProbeLevelTransform3 class
getChipType.AffymetrixCelFile

Gets the chip type for this CEL file
bgAdjustGcrma.AffymetrixCelFile

Applies probe sequence based background correction to a CEL file
TransformReport

The TransformReport class
QuantileNormalization

The QuantileNormalization class
QualityAssessmentSet

The QualityAssessmentSet class
process.GcRmaBackgroundCorrection

Performs background correction
extractAffyBatch.AffymetrixCelSet

Extracts an in-memory AffyBatch object from the CEL set
ExonChipEffectSet

The ExonChipEffectSet class
ScaleNormalization

The ScaleNormalization class
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
CnChipEffectFile

The CnChipEffectFile class
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
bgAdjustRma.AffymetrixCelSet

Applies RMA background correction to a set of CEL files
HetLogAddPlm

The HetLogAddPlm class
bpmapCluster2Cdf

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

Gets the cell indices of allele pairs
CnPlm

The CnPlm class
getDataSet.ArrayExplorer

Gets the data set
bgAdjustRma.AffymetrixCelFile

Applies normExp background correction to a CEL file
doFIRMA.AffymetrixCelSet

Finding Isoforms using Robust Multichip Analysis (FIRMA)
getAM.ChipEffectFile

Gets the log-intensities and log-ratios of chip effects for two arrays
DChipGenomeInformation

The DChipGenomeInformation class
getPositions.GenomeInformation

Gets the physical positions for a set of units
getName.TransformReport

Gets the name of the output data set
fit.ProbeLevelModel

Estimates the model parameters
DChipDcpFile

The DChipDcpFile class
RmaPlm

The RmaPlm class
FragmentLengthNormalization

The FragmentLengthNormalization class
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
getAlias.GenericReporter

Gets the alias of the report
importFromDChip.AffymetrixCelSet

Imports dChip-exported CEL files
plotMvsX.AffymetrixCelFile

Plots log-ratio versus another variable in a scatter plot
as.AffymetrixCnChpSet.AffymetrixCnChpSet

Coerce an object to an AffymetrixCnChpSet object
as.character.AffymetrixCelSet

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

Gets the CDF structure for this model
UnitModel

The UnitModel class
getName.Model

Gets the name of the output data set
byChipType.SnpInformation

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

The AffymetrixCnChpSet class
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
convert.AffymetrixCdfFile

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

The MultiArrayUnitModel class
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
isSnpChip.AffymetrixCdfFile

Static method to check if a chip is a mapping (SNP) chip
clearData.AffymetrixCelFile

Clears all or a subset of the fields in a CEL file
GcContentNormalization2

The GcContentNormalization2 class
process.ReseqCrosstalkCalibration

Calibrates the data set
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
setCdf.AffymetrixCelSet

Sets the CDF structure for this CEL set
findByChipType.AffymetrixCdfFile

Locates a CDF file from its chip type
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
getCdf.AffymetrixCelSet

Gets the CDF structure for this CEL set
getCellIndices.AffymetrixCdfFile

Gets the cell indices unit by unit
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
GcContentNormalization

The GcContentNormalization class
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
isPm.AffymetrixCdfFile

Checks which cells (probes) are PMs and not
SmoothMultiarrayModel

The SmoothMultiarrayModel class
getAverageFile.AffymetrixCelSet

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

The AvgSnpPlm class
convertUnits.AffymetrixCdfFile

Gets and validates unit indices
getFitUnitGroupFunction.MultiArrayUnitModel

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

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

Calibrates the data set
setRestructor.AffymetrixCdfFile

Specifies a function through which
getFitUnitGroupFunction.RmaPlm

Gets the low-level function that fits the PLM
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
getCellIndices.UnitModel

Gets the cell indices unit by unit
getFitUnitGroupFunction.AffinePlm

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

Normalizes the data set
GenomeInformation

The GenomeInformation class
fitQuantileNormFcn.AffymetrixCelFile

Fits quantile normalization functions for the arrays in the data set
QualityAssessmentFile

The QualityAssessmentFile class
setAlias.Model

Sets the name alias for the model
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
SnpProbeAffinityFile

The SnpProbeAffinityFile class
readCdfDataFrame

Reads units (probesets) from an Affymetrix CDF file
readUnits.MultiArrayUnitModel

Reads data unit by unit
ResidualSet

The ResidualSet class
byChipType.GenomeInformation

Static method to define a genome information set by chip type
getResiduals.QualityAssessmentModel

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

Calculates probe affinities from sequence
BackgroundCorrection

The BackgroundCorrection class
getData.SnpInformation

Gets all or a subset of the genome information data
getFitUnitGroupFunction.MbeiPlm

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

Gets the tags of the output data set
QualityAssessmentModel

The QualityAssessmentModel class
getChipType.SnpInformation

Gets the chip type of this genome information set
getFitUnitGroupFunction.SingleArrayUnitModel

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

Gets the transformed data set
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
bgAdjustOptical.AffymetrixCelFile

Applies optical background correction to a CEL file
allocateFromCdf.AromaUnitTabularBinaryFile

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
process.FragmentEquivalentClassNormalization

Normalizes the data set
ChipEffectTransform

The ChipEffectTransform class
plotDensity.AffymetrixCelFile

Plots the density of the probe signals on the array
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
MbeiPlm

The MbeiPlm class
getTags.TransformReport

Gets the tags of the output data set
getHeader.CnagCfhFile

Gets the header of the CEL file
fromCdf.SnpInformation

Static method to define a genome information set from a CDF
getRootPath.Model

Gets the root path of this model
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
DChipCdfBinFile

The DChipCdfBinFile class
MbeiCnPlm

The MbeiCnPlm class
getAlleleProbePairs.AffymetrixCdfFile

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

The NormExpBackgroundCorrection class
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
getDataSet.Model

Gets the input data set for this model
process.AdditiveCovariatesNormalization

Normalizes the data set
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
setAlias.GenericReporter

Sets the alias of the report
getName.GenericReporter

Gets the name of the explorer
getFitUnitGroupFunction.FirmaModel

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

The WeightsSet class
getFullName.TransformReport

Gets the full name of the output data set
getChipType.CnagCfhFile

Gets the chip type for this CEL file
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
importFromApt.CnChipEffectSet

Imports copy-number estimates from an APT summary file
getChipEffectSet.AlleleSummation

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

Processes the data set
fromDataFile.ChipEffectFile

Retrive an existing CEL file, or create from CDF template if missing
CnChipEffectSet

The CnChipEffectSet class
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
bgAdjustGcrma.AffymetrixCelSet

Applies probe sequence based background correction to a set of CEL files
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
process.LimmaBackgroundCorrection

Performs background correction
fromFile.AromaChipTypeAnnotationFile

Sets up an AromaChipTypeAnnotationFile
getAlleleProbePairs3.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
getAverageFile.CnagCfhSet

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

Gets the header of the annotation file
getWeights.QualityAssessmentModel

Calculates the weights from the robust fit to a probe-level model
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
getPath.Model

Gets the path of this model
process.GenericReporter

Generates report
extractMatrix.AffymetrixCelSet

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

Gets the CDF structure for this CEL file
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
getXAM.ChipEffectSet

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

The ExonRmaPlm class
nbrOfArrays.CnagCfhSet

Gets the number of arrays in the file set
getXAM.ChipEffectFile

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

Normalizes the data set
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
LinearModelProbeSequenceNormalization

The LinearModelProbeSequenceNormalization class
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
extractDataFrame.ParameterCelSet

Extract data as a data.frame for a set of arrays
getHeader.AffymetrixCelFile

Gets the header of the CEL file
process.BackgroundCorrection

Processes the data set
SingleArrayUnitModel

The SingleArrayUnitModel class
fromFile.CnagCfhFile

Defines an CnagCfhFile object from a CFH file
process.RmaBackgroundCorrection

Performs background correction
getFirmaSet.FirmaModel

Gets the set of FIRMA results for this model
process.ScaleNormalization

Normalizes the data set
getAlias.Model

Gets the name alias for the model
SnpPlm

The SnpPlm interface class
readUnits.CnagCfhFile

Reads CEL data unit by unit
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
getTags.GenericReporter

Gets the tags of the reporter
getSnpNames.AffymetrixCdfFile

Gets the names of the SNP units
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
setTags.Model

Sets the tags to be appended
getGenomeInformation.AffymetrixCdfFile

Gets genome information for this chip type
verify.SnpInformation

Verifies the correctness of the underlying file
process.ArrayExplorer

Generates image files, scripts and dynamic pages for the explorer
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
getChipType.GenomeInformation

Gets the chip type of this genome information set
normalizeQuantile.AffymetrixCelFile

Normalizes the probe intensities to a target empirical distribution
aroma.affymetrix-package

Package aroma.affymetrix
getImage.AffymetrixCelFile

Creates an RGB Image object from a CEL file
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
nbrOfArrays.DChipDcpSet

Gets the number of arrays in the file set
writeImage.AffymetrixCelFile

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

Reads CEL data unit by unit
byChipType.DChipSnpInformation

Defines a DChipSnpInformation object by chip type
process.ChipEffectGroupMerge

Normalizes the data set
process.ScaleNormalization3

Normalizes the data set
process.OpticalBackgroundCorrection

Performs background correction
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
readUnits.SingleArrayUnitModel

Reads data unit by unit
fit.SingleArrayUnitModel

Estimates the model parameters
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
setCdf.CnagCfhFile

Sets the CDF structure for this CEL file
setArrays.ArrayExplorer

Sets the arrays
getFitUnitGroupFunction.ExonRmaPlm

Gets the low-level function that fits the Exon PLM
nbrOfArrays.AffymetrixCelSet

Gets the number of arrays in the file set
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
process.UnitTypeScaleNormalization

Normalizes the data set
smoothScatterMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a smooth scatter plot
updateUnits.AffymetrixCelFile

Updates CEL data unit by unit
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
AffineCnPlm

The AffineCnPlm class
CrlmmParametersSet

The CrlmmParametersSet class
ChipEffectFile

The ChipEffectFile class
MatNormalization

The MatNormalization class
SpatialReporter

The SpatialReporter class
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
importFromDChip.CnChipEffectSet

Imports copy-number estimates from a dChip result file
process.MatNormalization

Normalizes the data set
process.AbstractProbeSequenceNormalization

Normalizes the data set
AffineSnpPlm

The AffineSnpPlm class
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
ReseqCrosstalkCalibration

The ReseqCrosstalkCalibration class
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
byChipType.AromaChipTypeAnnotationFile

Defines an AromaChipTypeAnnotationFile object by chip type
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
createUniqueCdf.AffymetrixCdfFile

Creates a unique-cell version of the CDF
fit.FirmaModel

Estimates the model parameters
getDataSet.AffymetrixCelSetReporter

Gets the data set
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
plotDensity.AffymetrixCelSet

Plots the densities of all samples
plotMvsA.AffymetrixCelFile

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

Normalizes the data set
process.FragmentLengthNormalization

Normalizes the data set
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
readRawData.AffymetrixCelFile

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