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aroma.core (version 1.8.0)

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

1.8.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

November 8th, 2010

Functions in aroma.core (1.8.0)

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

display.Explorer

Displays the explorer in the default browser

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The BinnedScatter class

AromaCellCpgFile

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

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

RawAlleleBFractions

The RawAlleleBFractions class

The RawCopyNumbers class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

The UnitTypesFile interface class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

The AromaPlatform class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

The AromaTransform class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

getChromosomes.ChromosomalModel

Gets the chromosomes available

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaTabularBinarySet

The AromaTabularBinarySet class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

estimateSds.CopyNumberChromosomalModel

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

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

segmentByMPCBS.RawGenomicSignals

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

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

fit.CopyNumberSegmentationModel

getTags.AromaTransform

Gets the tags of the output data set

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

The HaarSegModel class

fit.CopyNumberChromosomalModel

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

The CbsModel class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitCallSet

The AromaUnitCallSet class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

The GladModel class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

ChromosomeExplorer

The ChromosomeExplorer class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

setAlias.Explorer

Sets the alias of the output set

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

getFullName.AromaTransform

Gets the full name of the output data set

setArrays.Explorer

Sets the arrays

AromaUnitTypesFile

The AromaUnitTypesFile class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

isDone.AromaTransform

Checks if the data set is processed or not

The Explorer class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaGenomeTextFile

The AromaGenomeTextFile class

downloadPackagePatch

Download a package patch

getModel.ChromosomeExplorer

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

RawSequenceReads

The RawSequenceReads class

setArrays.ChromosomeExplorer

Sets the arrays

RawGenomicSignals

The RawGenomicSignals class

getAlias.Explorer

Gets the alias of the output set

doCBS.character

Performs CBS segmentation on a data set

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

writeFooter.AromaTabularBinaryFile

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

getTags.Explorer

Gets the tags of the explorer

getName.AromaTransform

Gets the name of the output data set

getOutputDataSet.AromaTransform

Gets the transformed data set

process.AromaTransform

Processes the data set

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The UnitNamesFile interface class

indexOf.UnitNamesFile

Gets the indices of units by their names

readFooter.AromaTabularBinaryFile

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

getNames.ChromosomalModel

Gets the names of the arrays

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

AromaUnitCallFile

The AromaUnitCallFile class

nbrOfArrays.Explorer

Gets the total number of arrays

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

getNames.Explorer

Gets the names of the input samples

Non-documented objects

Non-documented objects

getName.Explorer

Gets the name of the explorer

aroma.core-package

Package aroma.core

RawCopyNumberModel

The RawCopyNumberModel class

getChipType.ChromosomalModel

Gets a label for all chip types merged

nbrOfArrays.ChromosomalModel

Gets the number of arrays

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

ChromosomalModel

The ChromosomalModel class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

findAnnotationData

Locates an annotation data file

getInputDataSet.AromaTransform

Gets the input data set

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getPath.AromaTransform

Gets the path of the output data set

Applies patches for a specific package