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aroma.core (version 2.1.4)

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

2.1.4

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

August 2nd, 2011

Functions in aroma.core (2.1.4)

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitCallFile

The AromaUnitCallFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

display.Explorer

Displays the explorer in the default browser

isDone.AromaTransform

Checks if the data set is processed or not

process.AromaTransform

Processes the data set

AromaGenomeTextFile

The AromaGenomeTextFile class

The AromaPlatform class

AromaTabularBinarySet

The AromaTabularBinarySet class

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

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

nbrOfArrays.Explorer

Gets the total number of arrays

setArrays.ChromosomeExplorer

Sets the arrays

AromaUnitTypesFile

The AromaUnitTypesFile class

RawGenomicSignals

The RawGenomicSignals class

getChipType.ChromosomalModel

Gets a label for all chip types merged

The BinnedScatter class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

writeFooter.AromaTabularBinaryFile

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

RawAlleleBFractions

The RawAlleleBFractions class

The RawCopyNumbers class

Non-documented objects

Non-documented objects

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

AromaTabularBinaryFile

The AromaTabularBinaryFile class

findAnnotationData

Locates an annotation data file

The UnitNamesFile interface class

getChromosomes.ChromosomalModel

Gets the chromosomes available

getPath.AromaTransform

Gets the path of the output data set

The AromaTransform class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

setArrays.Explorer

Sets the arrays

getInputDataSet.AromaTransform

Gets the input data set

setAlias.Explorer

Sets the alias of the output set

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

The Explorer class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

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

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

getNames.ChromosomalModel

Gets the names of the arrays

The HaarSegModel class

AromaCellCpgFile

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

fit.CopyNumberSegmentationModel

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

aroma.core-package

Package aroma.core

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getName.Explorer

Gets the name of the explorer

ChromosomeExplorer

The ChromosomeExplorer class

fit.CopyNumberChromosomalModel

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

segmentByMPCBS.RawGenomicSignals

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

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

getFullName.AromaTransform

Gets the full name of the output data set

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getName.AromaTransform

Gets the name of the output data set

getNames.Explorer

Gets the names of the input samples

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

AromaUnitCallSet

The AromaUnitCallSet class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

ChromosomalModel

The ChromosomalModel class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

RawSequenceReads

The RawSequenceReads class

indexOf.UnitNamesFile

Gets the indices of units by their names

estimateSds.CopyNumberChromosomalModel

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

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

The GladModel class

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

Applies patches for a specific package

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getTags.Explorer

Gets the tags of the explorer

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

readFooter.AromaTabularBinaryFile

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

The CbsModel class

downloadPackagePatch

Download a package patch

RawCopyNumberModel

The RawCopyNumberModel class

The UnitTypesFile interface class

getTags.AromaTransform

Gets the tags of the output data set

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getModel.ChromosomeExplorer

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

getOutputDataSet.AromaTransform

Gets the transformed data set

nbrOfArrays.ChromosomalModel

Gets the number of arrays

doCBS.character

Performs CBS segmentation on a data set

getAlias.Explorer

Gets the alias of the output set