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aroma.core

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

Functions (132)

AbstractCNData

The AbstractCNData class

AbstractPSCNData

The AbstractPSCNData class

AromaCellCpgFile

A binary file holding local CpG density for each cell (probe/feature)

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaPlatform

The AromaPlatform class

AromaPlatformInterface

The AromaPlatformInterface class

AromaRepository

The AromaRepository class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaTransform

The AromaTransform class

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitTypesFile

The AromaUnitTypesFile class

BinnedScatter

The BinnedScatter class

CacheKeyInterface

The CacheKeyInterface class interface

CbsModel

The CbsModel class

ChromosomalModel

The ChromosomalModel class

ChromosomeExplorer

The ChromosomeExplorer class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

Explorer

The Explorer class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

GladModel

The GladModel class

HaarSegModel

The HaarSegModel class

Non-documented_objects

Non-documented objects

NonPairedPSCNData

The NonPairedPSCNData class

PairedPSCNData

The PairedPSCNData class

ParametersInterface

The ParametersInterface class interface

RawAlleleBFractions

The RawAlleleBFractions class

RawCopyNumberModel

The RawCopyNumberModel class

RawCopyNumbers

The RawCopyNumbers class

RawGenomicSignals

The RawGenomicSignals class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

RawSequenceReads

The RawSequenceReads class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

UnitNamesFile

The UnitNamesFile interface class

UnitTypesFile

The UnitTypesFile interface class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

aroma.core-package

Package aroma.core

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

display.Explorer

Displays the explorer in the default browser

doCBS

Performs Circular Binary Segmentation (CBS) on a data set

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

downloadFile.AromaRepository

Download a particular file from the repository

estimateSds.CopyNumberChromosomalModel

Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

exportAromaUnitPscnBinarySet

Export total and allele B signal data sets as a unified parent-specific copy number signal data set

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

findAnnotationData

Locates an annotation data file

findAnnotationDataByChipType

Locates an annotation data file by its chip type

findFilesTodo.AromaTransform

Finds files in the data set still not processed

fit.CopyNumberChromosomalModel

Fits the model

fit.CopyNumberSegmentationModel

Fits the model

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

getAlias.Explorer

Gets the alias of the output set

getAromaPlatform.AromaPlatformInterface

Gets the platform

getCacheKey.CacheKeyInterface

Gets a list of cache key items

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

getChipType.AromaPlatformInterface

Gets the chip type

getChipType.ChromosomalModel

Gets a label for all chip types merged

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getFullName.AromaTransform

Gets the full name of the output data set

getInputDataSet.AromaTransform

Gets the input data set

getModel.ChromosomeExplorer

Gets the model

getName.AromaTransform

Gets the name of the output data set

getName.Explorer

Gets the name of the explorer

getNames.ChromosomalModel

Gets the names of the arrays

getNames.Explorer

Gets the names of the input samples

getOutputDataSet.AromaTransform

Gets the transformed data set

getParameters.ParametersInterface

Gets a list of parameters

getParametersAsString.ParametersInterface

Gets the parameters as character

getPath.AromaTransform

Gets the path of the output directory

getPath.Explorer

Gets the path of the output directory

getPlatform.AromaPlatformInterface

Gets the platform

getRootPath.AromaTransform

Gets the root path of the output directory

getRootPath.Explorer

Gets the root path of the output directory

getTags.AromaTransform

Gets the tags of the output data set

getTags.Explorer

Gets the tags of the explorer

getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class

indexOf.UnitNamesFile

Gets the indices of units by their names

isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible

isDone.AromaTransform

Checks if the data set is processed or not

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfArrays.Explorer

Gets the total number of arrays

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

process.AromaTransform

Processes the data set

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

processTime

Gets the running time of the R process and its children processes

readFooter.AromaTabularBinaryFile

Reads the file footer in XML format into a named nested list

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

segmentByMPCBS.RawGenomicSignals

Segment copy numbers using the multi-platform CBS (mpCBS) method

setAlias.Explorer

Sets the alias of the output set

setArrays.ChromosomeExplorer

Sets the arrays

setArrays.Explorer

Sets the arrays

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

writeFooter.AromaTabularBinaryFile

Writes a named nested list to the file footer in XML format

aroma.core

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

v3.2.2
LGPL (>= 2.1)
Authors
Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Initial release

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