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aroma.affymetrix (version 2.11.1)

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 disk space that limits the number of arrays that can be analyzed.

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Version

Install

install.packages('aroma.affymetrix')

Monthly Downloads

608

Version

2.11.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

October 18th, 2013

Functions in aroma.affymetrix (2.11.1)

AffymetrixCdfFile

The AffymetrixCdfFile class
MbeiSnpPlm

The MbeiSnpPlm class
aroma.affymetrix-package

Package aroma.affymetrix
WeightsSet

The WeightsSet class
CrlmmParametersSet

The CrlmmParametersSet class
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
GcContentNormalization

The GcContentNormalization class
AffymetrixCelFile$clearData

Clears all or a subset of the fields in a CEL file
UgpGenomeInformation$byChipType

Defines a UgpGenomeInformation object by chip type
AffinePlm

The AffinePlm class
AromaUnitTabularBinaryFile$allocateFromCdf

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
AffymetrixPgfFile

The AffymetrixPgfFile class
GenericReporter

The GenericReporter class
CnPlm

The CnPlm class
DChipCdfBinFile

The DChipCdfBinFile class
ResidualFile

The ResidualFile class
ParameterCelFile

The ParameterCelFile class
SnpInformation

The SnpInformation class
BaseCountNormalization

The BaseCountNormalization class
ChipEffectFile

The ChipEffectFile class
bgAdjustGcrma.AffymetrixCelFile

Applies probe sequence based background correction to a CEL file
ProbeLevelTransform3

The ProbeLevelTransform3 class
extractAffyBatch.AffymetrixCelSet

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

The ReseqCrosstalkCalibration class
getChipType.CnagCfhFile

Gets the chip type for this CEL file
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
getOutputDataSet.Transform

Gets the transformed data set
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
AffineCnPlm

The AffineCnPlm class
getTags.Model

Gets the tags of the output data set
ChipEffectSet

The ChipEffectSet class
SingleArrayUnitModel

The SingleArrayUnitModel class
AvgSnpPlm

The AvgSnpPlm class
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
AffymetrixCelFile$fromFile

Defines an AffymetrixCelFile object from a CEL file
AffymetrixCnChpSet

The AffymetrixCnChpSet class
AffymetrixCdfFile$findByChipType

Locates a CDF file from its chip type
CnChipEffectSet

The CnChipEffectSet class
BasePositionNormalization

The BasePositionNormalization class
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
FirmaFile

The FirmaFile class
fit.SingleArrayUnitModel

Estimates the model parameters
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
getFitUnitGroupFunction.FirmaModel

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

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

Static method to check if a CDF is for a resequencing (CustomSeq) chip
QuantileNormalization

The QuantileNormalization class
AffineSnpPlm

The AffineSnpPlm class
bgAdjustRma.AffymetrixCelFile

Applies normExp background correction to a CEL file
DChipDcpSet

The DChipDcpSet class
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
SmoothMultiarrayModel

The SmoothMultiarrayModel class
bgAdjustGcrma.AffymetrixCelSet

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

The FirmaSet class
AlleleSummation

The AlleleSummation class
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
bpmapCluster2Cdf

Creates a CDF from tiling-array BPMAP file
QualityAssessmentFile

The QualityAssessmentFile class
AffymetrixPgfFile$findByChipType

Locates a PGF file from its chip type
AromaChipTypeAnnotationFile

The AromaChipTypeAnnotationFile class
SpatialReporter

The SpatialReporter class
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
AffymetrixCelFile$allocateFromCdf

Creates an empty CEL file from a template CDF
CrlmmParametersFile

The CrlmmParametersFile class
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
SnpChipEffectSet

The SnpChipEffectSet class
AvgCnPlm

The AvgCnPlm class
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
ChipEffectTransform

The ChipEffectTransform class
doCRMAv2

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

The AffymetrixFileSet class
getChipEffectSet.AlleleSummation

Gets the set of chip effects for this model
FragmentLengthNormalization

The FragmentLengthNormalization class
getDataSet.AffymetrixCelSetReporter

Gets the data set
findUnitsTodo.FirmaModel

Identifies non-fitted units
DChipQuantileNormalization

The DChipQuantileNormalization class
ExonChipEffectFile

The ExonChipEffectFile class
fitQuantileNormFcn.AffymetrixCelFile

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

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

Coerce an object to an AffymetrixCelSet object
AromaChipTypeAnnotationFile$fromFile

Sets up an AromaChipTypeAnnotationFile
TransformReport

The TransformReport class
getGenomeInformation.AffymetrixCdfFile

Gets genome information for this chip type
HetLogAddPlm

The HetLogAddPlm class
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
writeImage.AffymetrixCelFile

Writes a spatial image of the signals in the CEL file
getAlias.GenericReporter

Gets the alias of the report
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
MultiArrayUnitModel

The MultiArrayUnitModel class
CnProbeAffinityFile

The CnProbeAffinityFile class
RmaBackgroundCorrection

The RmaBackgroundCorrection class
HetLogAddCnPlm

The HetLogAddCnPlm class
MultiArrayUnitModel$getFitUnitGroupFunction

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

Estimates the model parameters
ProbeLevelTransform

The ProbeLevelTransform class
computeAffinities.AffymetrixCdfFile

Calculates probe affinities from sequence
BackgroundCorrection

The BackgroundCorrection class
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
getInputDataSet.TransformReport

Gets the source data set
getCellIndices.SnpProbeAffinityFile

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

The ParameterCelSet class
DChipDcpFile

The DChipDcpFile class
findUnitsTodo.UnitModel

Identifies non-fitted units
ExonProbeAffinityFile

The ExonProbeAffinityFile class
doGCRMA

Robust Multichip Analysis (GCRMA)
getCellIndices.AffymetrixCdfFile

Gets the cell indices unit by unit
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
getTags.GenericReporter

Gets the tags of the reporter
process.LimmaBackgroundCorrection

Performs background correction
SnpChipEffectFile

The SnpChipEffectFile class
getName.TransformReport

Gets the name of the output data set
getCellIndices.SnpChipEffectFile

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

The QualityAssessmentModel class
getFullName.Model

Gets the full name of the output set
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
WeightsFile

The WeightsFile class
AvgPlm

The AvgPlm class
getPath.Model

Gets the path of this model
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
UnitModel

The UnitModel class
getHeader.AffymetrixCdfFile

Gets the header of the CDF file
nbrOfArrays.AffymetrixCelSet

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

Gets the chip type for this CEL file
SnpInformation$fromCdf

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

The DChipSnpInformation class
getCdf.Model

Gets the CDF structure for this model
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
getFitUnitGroupFunction.AffinePlm

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

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

The MbeiCnPlm class
Model

The Model class
AffymetrixFile

The abstract AffymetrixFile class
getCellIndices.CnProbeAffinityFile

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

Gets the cell indices of allele pairs
getCellIndices.ExonProbeAffinityFile

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

Finding Isoforms using Robust Multichip Analysis (FIRMA)
getCellIndices.ResidualFile

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

The LinearModelProbeSequenceNormalization class
getDataSet.ArrayExplorer

Gets the data set
getCellIndices.ChipEffectFile

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

The DChipGenomeInformation class
getHeader.AffymetrixCelFile

Gets the header of the CEL file
extractFeatureSet.AffymetrixCelSet

Extracts CEL signals an in-memory FeatureSet object
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
AffymetrixPgfFile$fromFile

Defines an AffymetrixPgfFile object from a PGF file
getData.SnpInformation

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

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

Static method to check if a chip is a mapping (SNP) chip
SingleArrayUnitModel$getFitUnitGroupFunction

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

The UnitTypeScaleNormalization class
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
getXAM.ChipEffectFile

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

Reads CEL data unit by unit
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
CnChipEffectSet$importFromDChip

Imports copy-number estimates from a dChip result file
setCdf.AffymetrixCelSet

Sets the CDF structure for this CEL set
plotMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a scatter plot
getPositions.GenomeInformation

Gets the physical positions for a set of units
GenomeInformation

The GenomeInformation class
nbrOfArrays.DChipDcpSet

Gets the number of arrays in the file set
nbrOfArrays.AffymetrixCnChpSet

Gets the number of arrays in the file set
ArrayExplorer

The ArrayExplorer class
getFullName.TransformReport

Gets the full name of the output data set
getTags.TransformReport

Gets the tags of the output data set
process.GcContentNormalization

Normalizes the data set
process.ReseqCrosstalkCalibration

Calibrates the data set
ScaleNormalization

The ScaleNormalization class
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
process.OpticalBackgroundCorrection

Performs background correction
CnChipEffectFile

The CnChipEffectFile class
SnpProbeAffinityFile

The SnpProbeAffinityFile class
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
process.ScaleNormalization

Normalizes the data set
as.character.AffymetrixCnChpSet

Returns a short string describing the set
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
RmaSnpPlm

The RmaSnpPlm class
GenomeInformation$byChipType

Static method to define a genome information set by chip type
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
UgpGenomeInformation

The UgpGenomeInformation class
getAlias.Model

Gets the name alias for the model
convert.AffymetrixCdfFile

Converts a CDF into the same CDF but with another format
getXAM.ChipEffectSet

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

Sets the CDF structure for this CEL file
setRestructor.AffymetrixCdfFile

Specifies a function through which
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
readUnits.SingleArrayUnitModel

Reads data unit by unit
updateUnits.AffymetrixCelFile

Updates CEL data unit by unit
verify.GenomeInformation

Verifies the correctness of the underlying file
process.GcRmaBackgroundCorrection

Performs background correction
ExonChipEffectSet

The ExonChipEffectSet class
process.AbstractProbeSequenceNormalization

Normalizes the data set
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
AffymetrixCelFile

The AffymetrixCelFile class
process.GenericReporter

Generates report
ChipEffectFile$fromDataFile

Retrive an existing CEL file, or create from CDF template if missing
setArrays.ArrayExplorer

Sets the arrays
process.ScaleNormalization3

Normalizes the data set
isPm.AffymetrixCdfFile

Checks which cells (probes) are PMs and not
getAlleleProbePairs3.AffymetrixCdfFile

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

Sets the name alias for the model
getAverageFile.CnagCfhSet

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

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

Defines a DChipSnpInformation object by chip type
getCdf.AffymetrixCelSet

Gets the CDF structure for this CEL set
getCellIndices.ExonChipEffectFile

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

Checks if two AffymetrixCdfFile objects are equal
AffymetrixFileSet$byPath

Defines an AffymetrixFileSet object by searching for Affymetrix files
fit.Model

Estimates the model parameters
getAM.ChipEffectSet

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

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

Robust Multichip Analysis (RMA)
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
ChipEffectGroupMerge

The ChipEffectGroupMerge class
ExonRmaPlm

The ExonRmaPlm class
getHeader.AffymetrixPgfFile

Gets the header of the PGF file
bgAdjustOptical.AffymetrixCelFile

Applies optical background correction to a CEL file
AffymetrixCelSet

The AffymetrixCelSet class
process.MatSmoothing

Processes the data set
readRawData.AffymetrixCelFile

Gets all or a subset of the fields in a CEL file
getFitUnitGroupFunction.AvgPlm

Gets the low-level function that fits the PLM
CnagCfhFile

The CnagCfhFile class
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
getCellIndices.UnitModel

Gets the cell indices unit by unit
extractDataFrame.ParameterCelSet

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

The HetLogAddSnpPlm class
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
doCRMAv1

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

Plots log-ratio versus log-intensity in a smooth scatter plot
getRootPath.Model

Gets the root path of this model
MatSmoothing

The MatSmoothing class
getUnitNames.AffymetrixPgfFile

Gets the names of each unit
getAM.ChipEffectFile

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

Gets the name of the output data set
QualityAssessmentSet

The QualityAssessmentSet class
CnagCfhFile$fromFile

Defines an CnagCfhFile object from a CFH file
FirmaModel

The FirmaModel class
getImage.AffymetrixCelFile

Creates an RGB Image object from a CEL file
ResidualSet

The ResidualSet class
convertUnits.AffymetrixCdfFile

Gets and validates unit indices
process.QuantileNormalization

Normalizes the data set
getPath.TransformReport

Gets the path of the output data set
MatNormalization

The MatNormalization class
CnChipEffectSet$importFromApt

Imports copy-number estimates from an APT summary file
getFitUnitGroupFunction.HetLogAddPlm

Gets the low-level function that fits the PLM
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
getCellIndices.CnChipEffectFile

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

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

Gets the CDF structure for this CEL file
getIntensities.AffymetrixCelSet

Gets cell intensities from a set of cells and a set of arrays
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
RmaCnPlm

The RmaCnPlm class
pdInfo2Cdf

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

Normalizes the data set
plotMvsX.AffymetrixCelFile

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

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

Gets the names of the SNP units
getName.GenericReporter

Gets the name of the explorer
process.FragmentLengthNormalization

Normalizes the data set
getChipType.GenomeInformation

Gets the chip type of this genome information set
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
getResiduals.QualityAssessmentModel

Calculates the residuals from a probe-level model
process.RmaBackgroundCorrection

Performs background correction
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
getOutputDataSet.TransformReport

Gets the transformed data set
AffymetrixCdfFile$fromFile

Defines an AffymetrixCdfFile object from a CDF file
plotBoxplotStats.list

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

The ProbeAffinityFile class
CnagCfhSet

The CnagCfhSet class
setTags.Model

Sets the tags to be appended
RmaPlm

The RmaPlm class
readUnits.MultiArrayUnitModel

Reads data unit by unit
readUnits.AffymetrixCelFile

Reads CEL data unit by unit
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
createUniqueCdf.AffymetrixCdfFile

Creates a unique-cell version of the CDF
getData.GenomeInformation

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

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

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

Calibrates the data set
extractMatrix.AffymetrixCelSet

Extract data as a matrix for a set of arrays
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
setAlias.GenericReporter

Sets the alias of the report
process.FragmentEquivalentClassNormalization

Normalizes the data set
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
getHeader.CnagCfhFile

Gets the header of the CEL file
getHeader.AromaChipTypeAnnotationFile

Gets the header of the annotation file
process.UnitTypeScaleNormalization

Normalizes the data set
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
plotDensity.AffymetrixCelSet

Plots the densities of all samples
process.BackgroundCorrection

Processes the data set
process.MatNormalization

Normalizes the data set
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
NormExpBackgroundCorrection

The NormExpBackgroundCorrection class
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
byChipType.SnpInformation

Static method to define a genome information set by chip type
fit.FirmaModel

Estimates the model parameters
getCellIndices.FirmaFile

Retrieves tree list of cell indices for a set of units
getDataSet.Model

Gets the input data set for this model
getFirmaSet.FirmaModel

Gets the set of FIRMA results for this model
getWeights.QualityAssessmentModel

Calculates the weights from the robust fit to a probe-level model
AffymetrixCelSet$importFromDChip

Imports dChip-exported CEL files
plotDensity.AffymetrixCelFile

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

Normalizes the data set
process.ChipEffectGroupMerge

Normalizes the data set
verify.SnpInformation

Verifies the correctness of the underlying file
GcContentNormalization2

The GcContentNormalization2 class
LimmaBackgroundCorrection

The LimmaBackgroundCorrection class
MbeiPlm

The MbeiPlm class
Non-documented objects

Non-documented objects
ProbeLevelModel

The ProbeLevelModel class
ScaleNormalization3

The ScaleNormalization3 class
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
SmoothRmaModel

The SmoothRmaModel class
SnpPlm

The SnpPlm interface class
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
as.AffymetrixCnChpSet.AffymetrixCnChpSet

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

Returns a short string describing the Affymetrix CEL set
AromaChipTypeAnnotationFile$byChipType

Defines an AromaChipTypeAnnotationFile object by chip type
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
getChipType.SnpInformation

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

Generates image files, scripts and dynamic pages for the explorer