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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.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

642

Version

3.3.1

License

LGPL (>= 2.1)

Issues

Pull Requests

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Repository

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

Homepage

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

Maintainer

Henrik Bengtsson

Last Published

February 19th, 2024

Functions in aroma.core (3.3.1)

AbstractPSCNData

The AbstractPSCNData class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaCellCpgFile

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

AromaRepository

The AromaRepository class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

The AromaTransform class

The AromaPlatform class

AromaPlatformInterface

The AromaPlatformInterface class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitCallFile

The AromaUnitCallFile class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The GladModel class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

The Explorer class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

RawGenomicSignals

The RawGenomicSignals class

The UnitNamesFile interface class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The CbsModel class

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

ChromosomalModel

The ChromosomalModel class

RawCopyNumberModel

The RawCopyNumberModel class

The BinnedScatter class

The RawCopyNumbers class

downloadFile.AromaRepository

Download a particular file from the repository

findAnnotationData

Locates an annotation data file

NonPairedPSCNData

The NonPairedPSCNData class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

The PairedPSCNData class

getChipType.AromaPlatformInterface

Gets the chip type

CacheKeyInterface

The CacheKeyInterface class interface

ChromosomeExplorer

The ChromosomeExplorer class

getChipType.ChromosomalModel

Gets a label for all chip types merged

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

aroma.core-package

Package aroma.core

SegmentedCopyNumbers

The SegmentedCopyNumbers class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getPlatform.AromaPlatformInterface

Gets the platform

ParametersInterface

The ParametersInterface class interface

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

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

Performs Circular Binary Segmentation (CBS) on a data set

getParameters.ParametersInterface

Gets a list of parameters

getRootPath.AromaTransform

Gets the root path of the output directory

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

The HaarSegModel class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

Non-documented objects

Non-documented objects

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

fit.CopyNumberSegmentationModel

exportAromaUnitPscnBinarySet

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

RawAlleleBFractions

The RawAlleleBFractions class

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

getParametersAsString.ParametersInterface

Gets the parameters as character

getAlias.Explorer

Gets the alias of the output set

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

readFooter.AromaTabularBinaryFile

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

RawSequenceReads

The RawSequenceReads class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getRootPath.Explorer

Gets the root path of the output directory

getAromaPlatform.AromaPlatformInterface

Gets the platform

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

getTags.AromaTransform

Gets the tags of the output data set

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

setAlias.Explorer

Sets the alias of the output set

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

setArrays.ChromosomeExplorer

Sets the arrays

The UnitTypesFile interface class

getModel.ChromosomeExplorer

segmentByMPCBS.RawGenomicSignals

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

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

process.AromaTransform

Processes the data set

writeFooter.AromaTabularBinaryFile

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

estimateSds.CopyNumberChromosomalModel

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

getName.AromaTransform

Gets the name of the output data set

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

getNames.Explorer

Gets the names of the input samples

findFilesTodo.AromaTransform

Finds files in the data set still not processed

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getOutputDataSet.AromaTransform

Gets the transformed data set

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

fit.CopyNumberChromosomalModel

getFullName.AromaTransform

Gets the full name of the output data set

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

getCacheKey.CacheKeyInterface

Gets a list of cache key items

getTags.Explorer

Gets the tags of the explorer

getInputDataSet.AromaTransform

Gets the input data set

getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class

getName.Explorer

Gets the name of the explorer

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

getNames.ChromosomalModel

Gets the names of the arrays

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

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

isDone.AromaTransform

Checks if the data set is processed or not

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

setArrays.Explorer

Sets the arrays

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfArrays.Explorer

Gets the total number of arrays

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

The AbstractCNData class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class