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aroma.core (version 2.4.1)

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

731

Version

2.4.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

January 12th, 2012

Functions in aroma.core (2.4.1)

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

The HaarSegModel class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaCellPositionFile

A binary file holding chromosome/position for each cell

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

AromaTabularBinaryFile

The AromaTabularBinaryFile class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

RawAlleleBFractions

The RawAlleleBFractions class

findAnnotationData

Locates an annotation data file

AromaUnitCallFile

The AromaUnitCallFile class

display.Explorer

Displays the explorer in the default browser

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

aroma.core-package

Package aroma.core

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

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getNames.Explorer

Gets the names of the input samples

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

ChromosomalModel

The ChromosomalModel class

ChromosomeExplorer

The ChromosomeExplorer class

getTags.AromaTransform

Gets the tags of the output data set

readFooter.AromaTabularBinaryFile

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

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

setAlias.Explorer

Sets the alias of the output set

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

RawGenomicSignals

The RawGenomicSignals class

getOutputDataSet.AromaTransform

Gets the transformed data set

AromaTabularBinarySet

The AromaTabularBinarySet class

nbrOfArrays.ChromosomalModel

Gets the number of arrays

downloadPackagePatch

Download a package patch

segmentByMPCBS.RawGenomicSignals

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

getNames.ChromosomalModel

Gets the names of the arrays

getInputDataSet.AromaTransform

Gets the input data set

AromaGenomeTextFile

The AromaGenomeTextFile class

setArrays.ChromosomeExplorer

Sets the arrays

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

getChromosomes.ChromosomalModel

Gets the chromosomes available

process.AromaTransform

Processes the data set

The UnitNamesFile interface class

fit.CopyNumberSegmentationModel

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

Non-documented objects

Non-documented objects

RawSequenceReads

The RawSequenceReads class

doCBS.character

Performs CBS segmentation on a data set

getModel.ChromosomeExplorer

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

getFullName.AromaTransform

Gets the full name of the output data set

getPath.AromaTransform

Gets the path of the output data set

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

The Explorer class

estimateSds.CopyNumberChromosomalModel

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

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

The RawCopyNumbers class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

getName.Explorer

Gets the name of the explorer

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitCallSet

The AromaUnitCallSet class

The BinnedScatter class

RawCopyNumberModel

The RawCopyNumberModel class

The AromaTransform class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

fit.CopyNumberChromosomalModel

isDone.AromaTransform

Checks if the data set is processed or not

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaCellCpgFile

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

getTags.Explorer

Gets the tags of the explorer

Applies patches for a specific package

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getAlias.Explorer

Gets the alias of the output set

nbrOfArrays.Explorer

Gets the total number of arrays

setArrays.Explorer

Sets the arrays

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitTypesFile

The AromaUnitTypesFile class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

writeFooter.AromaTabularBinaryFile

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

The AromaPlatform class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

The GladModel class

The UnitTypesFile interface class

getName.AromaTransform

Gets the name of the output data set

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

getChipType.ChromosomalModel

Gets a label for all chip types merged

The CbsModel class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method