Learn R Programming

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

Installation

R package aroma.core is available on CRAN and can be installed in R as:

install.packages("aroma.core")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/aroma.core", ref="develop")

This will install the package from source.

Copy Link

Version

Install

install.packages('aroma.core')

Monthly Downloads

674

Version

3.3.2

License

LGPL (>= 2.1)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/HenrikBengtsson/aroma.core

Homepage

https://www.aroma-project.org/

Maintainer

Henrik Bengtsson

Last Published

August 18th, 2025

Functions in aroma.core (3.3.2)

AromaPlatformInterface

The AromaPlatformInterface class

AromaRepository

The AromaRepository class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaTabularBinarySet

The AromaTabularBinarySet class

The AromaPlatform class

AromaUnitCallSet

The AromaUnitCallSet class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

The AromaTransform class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

The BinnedScatter class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

ChromosomeExplorer

The ChromosomeExplorer class

CacheKeyInterface

The CacheKeyInterface class interface

The CbsModel class

The GladModel class

ChromosomalModel

The ChromosomalModel class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

The Explorer class

RawGenomicSignals

The RawGenomicSignals class

The RawCopyNumbers class

The PairedPSCNData class

The HaarSegModel class

NonPairedPSCNData

The NonPairedPSCNData class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

RawCopyNumberModel

The RawCopyNumberModel class

RawAlleleBFractions

The RawAlleleBFractions class

ParametersInterface

The ParametersInterface class interface

Non-documented objects

Non-documented objects

aroma.core-package

Package aroma.core

The UnitNamesFile interface class

The UnitTypesFile interface class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

RawSequenceReads

The RawSequenceReads class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

Performs Circular Binary Segmentation (CBS) on a data set

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

downloadFile.AromaRepository

Download a particular file from the repository

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

estimateSds.CopyNumberChromosomalModel

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

display.Explorer

Displays the explorer in the default browser

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

exportAromaUnitPscnBinarySet

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

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

fit.CopyNumberSegmentationModel

findFilesTodo.AromaTransform

Finds files in the data set still not processed

getAlias.Explorer

Gets the alias of the output set

fit.CopyNumberChromosomalModel

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

findAnnotationDataByChipType

Locates an annotation data file by its chip type

findAnnotationData

Locates an annotation data file

getFullName.AromaTransform

Gets the full name of the output data set

getInputDataSet.AromaTransform

Gets the input data set

getCacheKey.CacheKeyInterface

Gets a list of cache key items

getAromaPlatform.AromaPlatformInterface

Gets the platform

getName.AromaTransform

Gets the name of the output data set

getModel.ChromosomeExplorer

getOutputDataSet.AromaTransform

Gets the transformed data set

getNames.Explorer

Gets the names of the input samples

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getParametersAsString.ParametersInterface

Gets the parameters as character

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getParameters.ParametersInterface

Gets a list of parameters

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getPath.AromaTransform

Gets the path of the output directory

getPath.Explorer

Gets the path of the output directory

indexOf.UnitNamesFile

Gets the indices of units by their names

isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible

nbrOfArrays.Explorer

Gets the total number of arrays

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

isDone.AromaTransform

Checks if the data set is processed or not

nbrOfArrays.ChromosomalModel

Gets the number of arrays

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

getChipType.AromaPlatformInterface

Gets the chip type

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

setArrays.Explorer

Sets the arrays

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getTags.AromaTransform

Gets the tags of the output data set

getName.Explorer

Gets the name of the explorer

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

getPlatform.AromaPlatformInterface

Gets the platform

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

readFooter.AromaTabularBinaryFile

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

segmentByMPCBS.RawGenomicSignals

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

getChipType.ChromosomalModel

Gets a label for all chip types merged

getRootPath.Explorer

Gets the root path of the output directory

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

getNames.ChromosomalModel

Gets the names of the arrays

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

writeFooter.AromaTabularBinaryFile

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

getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class

getTags.Explorer

Gets the tags of the explorer

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

getRootPath.AromaTransform

Gets the root path of the output directory

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

process.AromaTransform

Processes the data set

setArrays.ChromosomeExplorer

Sets the arrays

setAlias.Explorer

Sets the alias of the output set

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AbstractCNData class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaCellCpgFile

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

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AbstractPSCNData

The AbstractPSCNData class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class