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aroma.core (version 1.7.0)

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

1.7.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

July 26th, 2010

Functions in aroma.core (1.7.0)

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

The CbsModel class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaUnitCallFile

The AromaUnitCallFile class

nbrOfArrays.ChromosomalModel

Gets the number of arrays

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

The RawCopyNumbers class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

estimateSds.CopyNumberChromosomalModel

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

getChromosomes.ChromosomalModel

Gets the chromosomes available

The Explorer class

ChromosomalModel

The ChromosomalModel class

downloadPackagePatch

Download a package patch

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

segmentByMPCBS.RawGenomicSignals

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

ChromosomeExplorer

The ChromosomeExplorer class

RawGenomicSignals

The RawGenomicSignals class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

The GladModel class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaUnitCallSet

The AromaUnitCallSet class

RawCopyNumberModel

The RawCopyNumberModel class

The UnitNamesFile interface class

getOutputDataSet.AromaTransform

Gets the transformed data set

getFullName.AromaTransform

Gets the full name of the output data set

nbrOfArrays.Explorer

Gets the total number of arrays

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

The AromaPlatform class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

fit.CopyNumberSegmentationModel

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

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

findAnnotationData

Locates an annotation data file

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

fit.CopyNumberChromosomalModel

aroma.core-package

Package aroma.core

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getName.Explorer

Gets the name of the explorer

getName.AromaTransform

Gets the name of the output data set

getAlias.Explorer

Gets the alias of the output set

setArrays.Explorer

Sets the arrays

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

display.Explorer

Displays the explorer in the default browser

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

setAlias.Explorer

Sets the alias of the output set

getModel.ChromosomeExplorer

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

The BinnedScatter class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getInputDataSet.AromaTransform

Gets the input data set

getTags.Explorer

Gets the tags of the explorer

The HaarSegModel class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

AromaUnitTypesFile

The AromaUnitTypesFile class

The AromaTransform class

isDone.AromaTransform

Checks if the data set is processed or not

process.AromaTransform

Processes the data set

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

SegmentedCopyNumbers

The SegmentedCopyNumbers class

AromaTabularBinarySet

The AromaTabularBinarySet class

Applies patches for a specific package

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

Non-documented objects

Non-documented objects

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

RawSequenceReads

The RawSequenceReads class

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

getTags.AromaTransform

Gets the tags of the output data set

writeFooter.AromaTabularBinaryFile

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

AromaCellCpgFile

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

The UnitTypesFile interface class

readFooter.AromaTabularBinaryFile

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

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getChipType.ChromosomalModel

Gets a label for all chip types merged

setArrays.ChromosomeExplorer

Sets the arrays

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getNames.ChromosomalModel

Gets the names of the arrays

getNames.Explorer

Gets the names of the input samples

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

RawAlleleBFractions

The RawAlleleBFractions class

getPath.AromaTransform

Gets the path of the output data set