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aroma.core (version 1.6.0)

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

1.6.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

May 16th, 2010

Functions in aroma.core (1.6.0)

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

The BinnedScatter class

The GladModel class

ChromosomalModel

The ChromosomalModel class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

RawAlleleBFractions

The RawAlleleBFractions class

AromaCellCpgFile

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

getChipType.ChromosomalModel

Gets a label for all chip types merged

RawCopyNumberModel

The RawCopyNumberModel class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

The AromaPlatform class

The CbsModel class

estimateSds.CopyNumberChromosomalModel

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

setAlias.Explorer

Sets the alias of the output set

nbrOfArrays.Explorer

Gets the total number of arrays

SegmentedCopyNumbers

The SegmentedCopyNumbers class

ChromosomeExplorer

The ChromosomeExplorer class

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

fit.CopyNumberSegmentationModel

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

The HaarSegModel class

aroma.core-package

Package aroma.core

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

The UnitTypesFile interface class

fit.CopyNumberChromosomalModel

getPath.AromaTransform

Gets the path of the output data set

getOutputDataSet.AromaTransform

Gets the transformed data set

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

getFullName.AromaTransform

Gets the full name of the output data set

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

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

AromaUnitCallFile

The AromaUnitCallFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

getInputDataSet.AromaTransform

Gets the input data set

getName.AromaTransform

Gets the name of the output data set

process.AromaTransform

Processes the data set

The UnitNamesFile interface class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

getName.Explorer

Gets the name of the explorer

AromaUnitTypesFile

The AromaUnitTypesFile class

RawGenomicSignals

The RawGenomicSignals class

getChromosomes.ChromosomalModel

Gets the chromosomes available

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

findAnnotationData

Locates an annotation data file

The RawCopyNumbers class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getNames.Explorer

Gets the names of the input samples

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

readFooter.AromaTabularBinaryFile

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

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

AromaCellPositionFile

A binary file holding chromosome/position for each cell

getTags.Explorer

Gets the tags of the explorer

AromaTabularBinarySet

The AromaTabularBinarySet class

indexOf.UnitNamesFile

Gets the indices of units by their names

RawSequenceReads

The RawSequenceReads class

nbrOfArrays.ChromosomalModel

Gets the number of arrays

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

getTags.AromaTransform

Gets the tags of the output data set

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

setArrays.ChromosomeExplorer

Sets the arrays

downloadPackagePatch

Download a package patch

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

setArrays.Explorer

Sets the arrays

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

AromaUnitCallSet

The AromaUnitCallSet class

getAlias.Explorer

Gets the alias of the output set

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

getModel.ChromosomeExplorer

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

segmentByMPCBS.RawGenomicSignals

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

The AromaTransform class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

The Explorer class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

writeFooter.AromaTabularBinaryFile

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

Non-documented objects

Non-documented objects

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

isDone.AromaTransform

Checks if the data set is processed or not

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

display.Explorer

Displays the explorer in the default browser

getNames.ChromosomalModel

Gets the names of the arrays

Applies patches for a specific package