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aroma.core (version 1.4.0)

Support package for aroma.affymetrix et al.

Description

This package is a private support package for aroma.affymetrix et al. The methods and classes of this package are independent of platform. Its API is in alpha and beta stage.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

1.4.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

January 7th, 2010

Functions in aroma.core (1.4.0)

RawAlleleBFractions

The RawAlleleBFractions class

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaTabularBinaryFile

The AromaTabularBinaryFile class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

The RawCopyNumbers class

The HaarSegModel class

Non-documented objects

Non-documented objects

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

The AromaTransform class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

The UnitTypesFile interface class

getPath.AromaTransform

Gets the path of the output data set

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

aroma.core-package

Package aroma.core

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

getModel.ChromosomeExplorer

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The AromaPlatform class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

nbrOfArrays.ChromosomalModel

Gets the number of arrays

getChipType.ChromosomalModel

Gets a label for all chip types merged

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

RawSequenceReads

The RawSequenceReads class

getName.AromaTransform

Gets the name of the output data set

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

isDone.AromaTransform

Checks if the data set is processed or not

AromaUnitTypesFile

The AromaUnitTypesFile class

The CbsModel class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

getFullName.AromaTransform

Gets the full name of the output data set

AromaUnitCallSet

The AromaUnitCallSet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

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

estimateSds.CopyNumberChromosomalModel

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

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

The Explorer class

downloadPackagePatch

Download a package patch

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

ChromosomalModel

The ChromosomalModel class

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

AromaTabularBinarySet

The AromaTabularBinarySet class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

getNames.ChromosomalModel

Gets the names of the arrays

findAnnotationData

Locates an annotation data file

AromaUnitCallFile

The AromaUnitCallFile class

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

RawGenomicSignals

The RawGenomicSignals class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

getNames.Explorer

Gets the names of the input samples

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getAlias.Explorer

Gets the alias of the output set

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

getChromosomes.ChromosomalModel

Gets the chromosomes available

Applies patches for a specific package

readFooter.AromaTabularBinaryFile

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

RawCopyNumberModel

The RawCopyNumberModel class

fit.CopyNumberChromosomalModel

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

nbrOfArrays.Explorer

Gets the total number of arrays

process.AromaTransform

Processes the data set

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

getOutputDataSet.AromaTransform

Gets the transformed data set

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

setArrays.ChromosomeExplorer

Sets the arrays

writeFooter.AromaTabularBinaryFile

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

fit.CopyNumberSegmentationModel

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

getName.Explorer

Gets the name of the explorer

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

getTags.AromaTransform

Gets the tags of the output data set

setArrays.Explorer

Sets the arrays

getTags.Explorer

Gets the tags of the explorer

setAlias.Explorer

Sets the alias of the output set

ChromosomeExplorer

The ChromosomeExplorer class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

The GladModel class

display.Explorer

Displays the explorer in the default browser

The UnitNamesFile interface class

getInputDataSet.AromaTransform

Gets the input data set

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

The BinnedScatter class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method