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aroma.core (version 2.6.0)

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

588

Version

2.6.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

September 6th, 2012

Functions in aroma.core (2.6.0)

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

The AbstractCNData class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaCellCpgFile

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

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

The UnitTypesFile interface class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getNames.Explorer

Gets the names of the input samples

ChromosomalModel

The ChromosomalModel class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getAlias.Explorer

Gets the alias of the output set

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaRepository

The AromaRepository class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

setArrays.Explorer

Sets the arrays

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

AromaUnitCallSet

The AromaUnitCallSet class

The RawCopyNumbers class

getChromosomes.ChromosomalModel

Gets the chromosomes available

ChromosomeExplorer

The ChromosomeExplorer class

Non-documented objects

Non-documented objects

fit.CopyNumberSegmentationModel

getName.AromaTransform

Gets the name of the output data set

findAnnotationDataByChipType

Locates an annotation data file by its chip type

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

The BinnedScatter class

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

estimateSds.CopyNumberChromosomalModel

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

fit.CopyNumberChromosomalModel

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

getInputDataSet.AromaTransform

Gets the input data set

getName.Explorer

Gets the name of the explorer

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AbstractPSCNData

The AbstractPSCNData class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

nbrOfArrays.ChromosomalModel

Gets the number of arrays

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getOutputDataSet.AromaTransform

Gets the transformed data set

AromaTabularBinarySet

The AromaTabularBinarySet class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

The UnitNamesFile interface class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaTabularBinaryFile

The AromaTabularBinaryFile class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

aroma.core-package

Package aroma.core

The HaarSegModel class

The GladModel class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

Applies patches for a specific package

findAnnotationData

Locates an annotation data file

RawGenomicSignals

The RawGenomicSignals class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

downloadFile.AromaRepository

Download a particular file from the reposity

The AromaTransform class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

The AromaPlatform class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getChipType.ChromosomalModel

Gets a label for all chip types merged

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getFullName.AromaTransform

Gets the full name of the output data set

getTags.Explorer

Gets the tags of the explorer

downloadPackagePatch

Download a package patch

AromaGenomeTextFile

The AromaGenomeTextFile class

getTags.AromaTransform

Gets the tags of the output data set

getNames.ChromosomalModel

Gets the names of the arrays

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

getPath.AromaTransform

Gets the path of the output data set

writeFooter.AromaTabularBinaryFile

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

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

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

setArrays.ChromosomeExplorer

Sets the arrays

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

display.Explorer

Displays the explorer in the default browser

readFooter.AromaTabularBinaryFile

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

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

RawAlleleBFractions

The RawAlleleBFractions class

RawCopyNumberModel

The RawCopyNumberModel class

The PairedPSCNData class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

process.AromaTransform

Processes the data set

setAlias.Explorer

Sets the alias of the output set

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

segmentByMPCBS.RawGenomicSignals

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

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

doCBS.character

Performs CBS segmentation on a data set

isDone.AromaTransform

Checks if the data set is processed or not

nbrOfArrays.Explorer

Gets the total number of arrays

The CbsModel class

The Explorer class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaUnitTypesFile

The AromaUnitTypesFile class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

RawSequenceReads

The RawSequenceReads class

getModel.ChromosomeExplorer

NonPairedPSCNData

The NonPairedPSCNData class