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aroma.core (version 2.5.0)

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.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

2.5.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

March 26th, 2012

Functions in aroma.core (2.5.0)

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

ChromosomeExplorer

The ChromosomeExplorer class

AromaGenomeTextFile

The AromaGenomeTextFile class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

AromaUnitTypesFile

The AromaUnitTypesFile class

The PairedPSCNData class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

The HaarSegModel class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaCellCpgFile

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

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

The UnitTypesFile interface class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getFullName.AromaTransform

Gets the full name of the output data set

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

The RawCopyNumbers class

estimateSds.CopyNumberChromosomalModel

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

readFooter.AromaTabularBinaryFile

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

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

The GladModel class

Applies patches for a specific package

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

fit.CopyNumberSegmentationModel

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

display.Explorer

Displays the explorer in the default browser

The AromaPlatform class

getChromosomes.ChromosomalModel

Gets the chromosomes available

The Explorer class

getPath.AromaTransform

Gets the path of the output data set

setAlias.Explorer

Sets the alias of the output set

findAnnotationDataByChipType

Locates an annotation data file by its chip type

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

The UnitNamesFile interface class

downloadPackagePatch

Download a package patch

Non-documented objects

Non-documented objects

RawSequenceReads

The RawSequenceReads class

AbstractPSCNData

The AbstractPSCNData class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

nbrOfArrays.ChromosomalModel

Gets the number of arrays

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaTabularBinarySet

The AromaTabularBinarySet class

findAnnotationData

Locates an annotation data file

getTags.Explorer

Gets the tags of the explorer

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

setArrays.Explorer

Sets the arrays

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getName.Explorer

Gets the name of the explorer

RawGenomicSignals

The RawGenomicSignals class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

NonPairedPSCNData

The NonPairedPSCNData class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

getAlias.Explorer

Gets the alias of the output set

SegmentedCopyNumbers

The SegmentedCopyNumbers class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

isDone.AromaTransform

Checks if the data set is processed or not

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The AromaTransform class

RawAlleleBFractions

The RawAlleleBFractions class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getChipType.ChromosomalModel

Gets a label for all chip types merged

setArrays.ChromosomeExplorer

Sets the arrays

writeFooter.AromaTabularBinaryFile

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

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

getTags.AromaTransform

Gets the tags of the output data set

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getNames.Explorer

Gets the names of the input samples

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

getModel.ChromosomeExplorer

getName.AromaTransform

Gets the name of the output data set

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

doCBS.character

Performs CBS segmentation on a data set

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

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

getNames.ChromosomalModel

Gets the names of the arrays

getInputDataSet.AromaTransform

Gets the input data set

process.AromaTransform

Processes the data set

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

fit.CopyNumberChromosomalModel

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

The CbsModel class

aroma.core-package

Package aroma.core

ChromosomalModel

The ChromosomalModel class

Weighted Median Absolute Deviation (MAD)

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitCallSet

The AromaUnitCallSet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

RawCopyNumberModel

The RawCopyNumberModel class

getOutputDataSet.AromaTransform

Gets the transformed data set

nbrOfArrays.Explorer

Gets the total number of arrays

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

segmentByMPCBS.RawGenomicSignals

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

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AbstractCNData class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

The BinnedScatter class