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aroma.core (version 2.1.0)

Core methods and classes used by aroma.* package part of The Aroma Project

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

588

Version

2.1.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

April 9th, 2011

Functions in aroma.core (2.1.0)

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

display.Explorer

Displays the explorer in the default browser

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

downloadPackagePatch

Download a package patch

The RawCopyNumbers class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getFullName.AromaTransform

Gets the full name of the output data set

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

segmentByMPCBS.RawGenomicSignals

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

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

Non-documented objects

Non-documented objects

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

AromaTabularBinaryFile

The AromaTabularBinaryFile class

fit.CopyNumberChromosomalModel

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

isDone.AromaTransform

Checks if the data set is processed or not

writeFooter.AromaTabularBinaryFile

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

ChromosomalModel

The ChromosomalModel class

aroma.core-package

Package aroma.core

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

getNames.ChromosomalModel

Gets the names of the arrays

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getPath.AromaTransform

Gets the path of the output data set

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getChromosomes.ChromosomalModel

Gets the chromosomes available

AromaCellCpgFile

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

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

The BinnedScatter class

AromaUnitCallSet

The AromaUnitCallSet class

RawSequenceReads

The RawSequenceReads class

getAlias.Explorer

Gets the alias of the output set

doCBS.character

Performs CBS segmentation on a data set

RawAlleleBFractions

The RawAlleleBFractions class

The UnitTypesFile interface class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

getTags.AromaTransform

Gets the tags of the output data set

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

fit.CopyNumberSegmentationModel

AromaTabularBinarySet

The AromaTabularBinarySet class

The AromaTransform class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

nbrOfArrays.ChromosomalModel

Gets the number of arrays

The Explorer class

findAnnotationData

Locates an annotation data file

readFooter.AromaTabularBinaryFile

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

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

setArrays.ChromosomeExplorer

Sets the arrays

The GladModel class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

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

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

RawGenomicSignals

The RawGenomicSignals class

nbrOfArrays.Explorer

Gets the total number of arrays

indexOf.UnitNamesFile

Gets the indices of units by their names

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

The CbsModel class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

getNames.Explorer

Gets the names of the input samples

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

getInputDataSet.AromaTransform

Gets the input data set

getChipType.ChromosomalModel

Gets a label for all chip types merged

Applies patches for a specific package

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

process.AromaTransform

Processes the data set

The AromaPlatform class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

getName.AromaTransform

Gets the name of the output data set

The UnitNamesFile interface class

setAlias.Explorer

Sets the alias of the output set

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

getName.Explorer

Gets the name of the explorer

getModel.ChromosomeExplorer

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

AromaCellPositionFile

A binary file holding chromosome/position for each cell

ChromosomeExplorer

The ChromosomeExplorer class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

setArrays.Explorer

Sets the arrays

getTags.Explorer

Gets the tags of the explorer

The HaarSegModel class

RawCopyNumberModel

The RawCopyNumberModel class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getOutputDataSet.AromaTransform

Gets the transformed data set