Learn R Programming

⚠️There's a newer version (3.3.2) of this package.Take me there.

aroma.core (version 2.9.0)

Core methods and classes used by aroma.* packages part of The Aroma Framework

Description

This package contains core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn. Its API should be considered to be in alpha and beta versions, and is mostly of interest to developers.

Copy Link

Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

2.9.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

April 25th, 2013

Functions in aroma.core (2.9.0)

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

getName.Explorer

Gets the name of the explorer

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

downloadPackagePatch

Download a package patch

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaTabularBinarySet

The AromaTabularBinarySet class

The Explorer class

AromaUnitTypesFile

The AromaUnitTypesFile class

NonPairedPSCNData

The NonPairedPSCNData class

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

The UnitNamesFile interface class

ParametersInterface

The ParametersInterface class interface

AromaCellCpgFile

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

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

RawCopyNumberModel

The RawCopyNumberModel class

The AromaPlatform class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

The UnitTypesFile interface class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getRootPath.AromaTransform

Gets the root path of the output directory

The HaarSegModel class

getChromosomes.ChromosomalModel

Gets the chromosomes available

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

getNames.Explorer

Gets the names of the input samples

writeFooter.AromaTabularBinaryFile

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

getNames.ChromosomalModel

Gets the names of the arrays

AromaUnitCallSet

The AromaUnitCallSet class

AromaRepository

The AromaRepository class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

RawSequenceReads

The RawSequenceReads class

aroma.core-package

Package aroma.core

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

RawAlleleBFractions

The RawAlleleBFractions class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

getModel.ChromosomeExplorer

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

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

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

CacheKeyInterface

The CacheKeyInterface class interface

findAnnotationData

Locates an annotation data file

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getInputDataSet.AromaTransform

Gets the input data set

AromaCellPositionFile

A binary file holding chromosome/position for each cell

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

getOutputDataSet.AromaTransform

Gets the transformed data set

getRootPath.Explorer

Gets the root path of the output directory

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

The AromaTransform class

setAlias.Explorer

Sets the alias of the output set

nbrOfArrays.ChromosomalModel

Gets the number of arrays

getPath.AromaTransform

Gets the path of the output directory

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

isDone.AromaTransform

Checks if the data set is processed or not

Non-documented objects

Non-documented objects

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

getCacheKey.CacheKeyInterface

Gets a list of cache key items

fit.CopyNumberChromosomalModel

getParametersAsString.ParametersInterface

Gets the parameters as character

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

setArrays.Explorer

Sets the arrays

The AbstractCNData class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

setArrays.ChromosomeExplorer

Sets the arrays

fit.CopyNumberSegmentationModel

nbrOfArrays.Explorer

Gets the total number of arrays

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getChipType.ChromosomalModel

Gets a label for all chip types merged

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

AbstractPSCNData

The AbstractPSCNData class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The RawCopyNumbers class

estimateSds.CopyNumberChromosomalModel

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

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

display.Explorer

Displays the explorer in the default browser

AromaUnitCallFile

The AromaUnitCallFile class

The CbsModel class

downloadFile.AromaRepository

Download a particular file from the reposity

getName.AromaTransform

Gets the name of the output data set

getParameters.ParametersInterface

Gets a list of parameters

getTags.AromaTransform

Gets the tags of the output data set

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

The GladModel class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

getTags.Explorer

Gets the tags of the explorer

Applies patches for a specific package

getAlias.Explorer

Gets the alias of the output set

getPath.Explorer

Gets the path of the output directory

getFullName.AromaTransform

Gets the full name of the output data set

segmentByMPCBS.RawGenomicSignals

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

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

ChromosomeExplorer

The ChromosomeExplorer class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

The BinnedScatter class

doCBS.character

Performs CBS segmentation on a data set

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

ChromosomalModel

The ChromosomalModel class

RawGenomicSignals

The RawGenomicSignals class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

readFooter.AromaTabularBinaryFile

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

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

process.AromaTransform

Processes the data set

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

The PairedPSCNData class

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaGenomeTextFile

The AromaGenomeTextFile class