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aroma.core (version 2.1.5)

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

2.1.5

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

August 31st, 2011

Functions in aroma.core (2.1.5)

The BinnedScatter class

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AromaPlatform class

The HaarSegModel class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

display.Explorer

Displays the explorer in the default browser

AromaCellCpgFile

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

getModel.ChromosomeExplorer

RawAlleleBFractions

The RawAlleleBFractions class

The CbsModel class

ChromosomeExplorer

The ChromosomeExplorer class

getNames.Explorer

Gets the names of the input samples

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

indexOf.UnitNamesFile

Gets the indices of units by their names

The GladModel class

AromaUnitTypesFile

The AromaUnitTypesFile class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

The Explorer class

getFullName.AromaTransform

Gets the full name of the output data set

findAnnotationDataByChipType

Locates an annotation data file by its chip type

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

RawSequenceReads

The RawSequenceReads class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getChromosomes.ChromosomalModel

Gets the chromosomes available

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getTags.AromaTransform

Gets the tags of the output data set

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getAlias.Explorer

Gets the alias of the output set

getTags.Explorer

Gets the tags of the explorer

getInputDataSet.AromaTransform

Gets the input data set

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

fit.CopyNumberChromosomalModel

doCBS.character

Performs CBS segmentation on a data set

aroma.core-package

Package aroma.core

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

RawGenomicSignals

The RawGenomicSignals class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

readFooter.AromaTabularBinaryFile

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

AromaUnitCallSet

The AromaUnitCallSet class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

setArrays.Explorer

Sets the arrays

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

setAlias.Explorer

Sets the alias of the output set

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

getPath.AromaTransform

Gets the path of the output data set

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

The UnitTypesFile interface class

Applies patches for a specific package

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

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

setArrays.ChromosomeExplorer

Sets the arrays

The RawCopyNumbers class

nbrOfArrays.Explorer

Gets the total number of arrays

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

RawCopyNumberModel

The RawCopyNumberModel class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

findAnnotationData

Locates an annotation data file

getChipType.ChromosomalModel

Gets a label for all chip types merged

segmentByMPCBS.RawGenomicSignals

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

getName.Explorer

Gets the name of the explorer

process.AromaTransform

Processes the data set

getOutputDataSet.AromaTransform

Gets the transformed data set

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

getNames.ChromosomalModel

Gets the names of the arrays

getName.AromaTransform

Gets the name of the output data set

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

Non-documented objects

Non-documented objects

estimateSds.CopyNumberChromosomalModel

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

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

isDone.AromaTransform

Checks if the data set is processed or not

The UnitNamesFile interface class

writeFooter.AromaTabularBinaryFile

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

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

The AromaTransform class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

ChromosomalModel

The ChromosomalModel class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

downloadPackagePatch

Download a package patch

AromaUnitCallFile

The AromaUnitCallFile class

fit.CopyNumberSegmentationModel