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aroma.core (version 2.11.0)

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 is mostly of interest to developers and is rarely used by end users directly.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

2.11.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

October 17th, 2013

Functions in aroma.core (2.11.0)

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

RawSequenceReads

The RawSequenceReads class

ChromosomeExplorer

The ChromosomeExplorer class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitCallFile

The AromaUnitCallFile class

The AromaPlatform class

RawAlleleBFractions

The RawAlleleBFractions class

The AbstractCNData class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

NonPairedPSCNData

The NonPairedPSCNData class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaRepository

The AromaRepository class

ChromosomalModel

The ChromosomalModel class

getInputDataSet.AromaTransform

Gets the input data set

downloadFile.AromaRepository

Download a particular file from the reposity

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

aroma.core-package

Package aroma.core

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaCellCpgFile

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

getAlias.Explorer

Gets the alias of the output set

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The GladModel class

nbrOfArrays.Explorer

Gets the total number of arrays

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitCallSet

The AromaUnitCallSet class

AromaTabularBinarySet

The AromaTabularBinarySet class

Performs Circular Binary Segmentation (CBS) on a data set

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

findAnnotationData

Locates an annotation data file

getModel.ChromosomeExplorer

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

fit.CopyNumberChromosomalModel

The CbsModel class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The HaarSegModel class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

RawCopyNumberModel

The RawCopyNumberModel class

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

getName.AromaTransform

Gets the name of the output data set

getParametersAsString.ParametersInterface

Gets the parameters as character

fit.CopyNumberSegmentationModel

downloadPackagePatch

Download a package patch

estimateSds.CopyNumberChromosomalModel

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

getRootPath.AromaTransform

Gets the root path of the output directory

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

The UnitTypesFile interface class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

Non-documented objects

Non-documented objects

process.AromaTransform

Processes the data set

getPath.Explorer

Gets the path of the output directory

Applies patches for a specific package

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

AromaGenomeTextFile

The AromaGenomeTextFile class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getOutputDataSet.AromaTransform

Gets the transformed data set

setArrays.Explorer

Sets the arrays

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AbstractPSCNData

The AbstractPSCNData class

readFooter.AromaTabularBinaryFile

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

getName.Explorer

Gets the name of the explorer

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

isDone.AromaTransform

Checks if the data set is processed or not

indexOf.UnitNamesFile

Gets the indices of units by their names

getTags.AromaTransform

Gets the tags of the output data set

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

The UnitNamesFile interface class

getNames.Explorer

Gets the names of the input samples

getFullName.AromaTransform

Gets the full name of the output data set

nbrOfArrays.ChromosomalModel

Gets the number of arrays

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

findFilesTodo.AromaTransform

Finds files in the data set still not processed

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

getChipType.ChromosomalModel

Gets a label for all chip types merged

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

segmentByMPCBS.RawGenomicSignals

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

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getParameters.ParametersInterface

Gets a list of parameters

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

writeFooter.AromaTabularBinaryFile

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

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

The PairedPSCNData class

The BinnedScatter class

setAlias.Explorer

Sets the alias of the output set

getNames.ChromosomalModel

Gets the names of the arrays

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

The RawCopyNumbers class

RawGenomicSignals

The RawGenomicSignals class

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

CacheKeyInterface

The CacheKeyInterface class interface

setArrays.ChromosomeExplorer

Sets the arrays

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

ParametersInterface

The ParametersInterface class interface

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The AromaTransform class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

display.Explorer

Displays the explorer in the default browser

The Explorer class

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

getCacheKey.CacheKeyInterface

Gets a list of cache key items

getTags.Explorer

Gets the tags of the explorer

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getRootPath.Explorer

Gets the root path of the output directory

getPath.AromaTransform

Gets the path of the output directory

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class