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aroma.core (version 1.5.0)

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

1.5.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

February 23rd, 2010

Functions in aroma.core (1.5.0)

fit.CopyNumberChromosomalModel

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

RawCopyNumberModel

The RawCopyNumberModel class

The AromaTransform class

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitTypesFile

The AromaUnitTypesFile class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaCellCpgFile

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

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

ChromosomeExplorer

The ChromosomeExplorer class

The Explorer class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

Non-documented objects

Non-documented objects

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

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

display.Explorer

Displays the explorer in the default browser

RawSequenceReads

The RawSequenceReads class

getModel.ChromosomeExplorer

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

The HaarSegModel class

AromaUnitCallSet

The AromaUnitCallSet class

isDone.AromaTransform

Checks if the data set is processed or not

getPath.AromaTransform

Gets the path of the output data set

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

The GladModel class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getFullName.AromaTransform

Gets the full name of the output data set

indexOf.UnitNamesFile

Gets the indices of units by their names

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

segmentByMPCBS.RawGenomicSignals

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

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

setArrays.ChromosomeExplorer

Sets the arrays

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

getNames.Explorer

Gets the names of the input samples

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

estimateSds.CopyNumberChromosomalModel

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

findAnnotationData

Locates an annotation data file

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getTags.Explorer

Gets the tags of the explorer

setAlias.Explorer

Sets the alias of the output set

process.AromaTransform

Processes the data set

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

The CbsModel class

downloadPackagePatch

Download a package patch

The UnitNamesFile interface class

The RawCopyNumbers class

getAlias.Explorer

Gets the alias of the output set

readFooter.AromaTabularBinaryFile

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

getOutputDataSet.AromaTransform

Gets the transformed data set

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

Applies patches for a specific package

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getNames.ChromosomalModel

Gets the names of the arrays

The UnitTypesFile interface class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getInputDataSet.AromaTransform

Gets the input data set

RawGenomicSignals

The RawGenomicSignals class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

getTags.AromaTransform

Gets the tags of the output data set

RawAlleleBFractions

The RawAlleleBFractions class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getChromosomes.ChromosomalModel

Gets the chromosomes available

fit.CopyNumberSegmentationModel

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

setArrays.Explorer

Sets the arrays

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

aroma.core-package

Package aroma.core

getName.Explorer

Gets the name of the explorer

nbrOfArrays.Explorer

Gets the total number of arrays

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

The BinnedScatter class

The AromaPlatform class

ChromosomalModel

The ChromosomalModel class

getChipType.ChromosomalModel

Gets a label for all chip types merged

getName.AromaTransform

Gets the name of the output data set

writeFooter.AromaTabularBinaryFile

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