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aroma.core (version 2.3.0)

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

2.3.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

November 2nd, 2011

Functions in aroma.core (2.3.0)

AromaTabularBinarySet

The AromaTabularBinarySet class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

display.Explorer

Displays the explorer in the default browser

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

fit.CopyNumberSegmentationModel

RawCopyNumberModel

The RawCopyNumberModel class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

The RawCopyNumbers class

nbrOfArrays.Explorer

Gets the total number of arrays

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getName.AromaTransform

Gets the name of the output data set

setArrays.Explorer

Sets the arrays

getChromosomes.ChromosomalModel

Gets the chromosomes available

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

getTags.Explorer

Gets the tags of the explorer

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getFullName.AromaTransform

Gets the full name of the output data set

The GladModel class

readFooter.AromaTabularBinaryFile

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

estimateSds.CopyNumberChromosomalModel

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

AromaCellPositionFile

A binary file holding chromosome/position for each cell

findAnnotationData

Locates an annotation data file

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

The UnitNamesFile interface class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getTags.AromaTransform

Gets the tags of the output data set

aroma.core-package

Package aroma.core

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaGenomeTextFile

The AromaGenomeTextFile class

process.AromaTransform

Processes the data set

segmentByMPCBS.RawGenomicSignals

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

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaTabularBinaryFile

The AromaTabularBinaryFile class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

AromaUnitTypesFile

The AromaUnitTypesFile class

setArrays.ChromosomeExplorer

Sets the arrays

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

The HaarSegModel class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

ChromosomalModel

The ChromosomalModel class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

getAlias.Explorer

Gets the alias of the output set

getNames.Explorer

Gets the names of the input samples

Non-documented objects

Non-documented objects

getNames.ChromosomalModel

Gets the names of the arrays

RawAlleleBFractions

The RawAlleleBFractions class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

getChipType.ChromosomalModel

Gets a label for all chip types merged

fit.CopyNumberChromosomalModel

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

getPath.AromaTransform

Gets the path of the output data set

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

The BinnedScatter class

writeFooter.AromaTabularBinaryFile

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

The UnitTypesFile interface class

AromaUnitCallFile

The AromaUnitCallFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaCellCpgFile

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

The CbsModel class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

The AromaPlatform class

RawGenomicSignals

The RawGenomicSignals class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

isDone.AromaTransform

Checks if the data set is processed or not

getModel.ChromosomeExplorer

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

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

The AromaTransform class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

RawSequenceReads

The RawSequenceReads class

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

ChromosomeExplorer

The ChromosomeExplorer class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

doCBS.character

Performs CBS segmentation on a data set

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

getName.Explorer

Gets the name of the explorer

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

The Explorer class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

nbrOfArrays.ChromosomalModel

Gets the number of arrays

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

getInputDataSet.AromaTransform

Gets the input data set

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

getOutputDataSet.AromaTransform

Gets the transformed data set

downloadPackagePatch

Download a package patch

setAlias.Explorer

Sets the alias of the output set

Applies patches for a specific package