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aroma.core (version 2.0.0)

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

2.0.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

February 17th, 2011

Functions in aroma.core (2.0.0)

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

getTags.Explorer

Gets the tags of the explorer

getModel.ChromosomeExplorer

getNames.Explorer

Gets the names of the input samples

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

The GladModel class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

Non-documented objects

Non-documented objects

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

The Explorer class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

AromaTabularBinarySet

The AromaTabularBinarySet class

downloadPackagePatch

Download a package patch

The CbsModel class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

AromaUnitTypesFile

The AromaUnitTypesFile class

ChromosomeExplorer

The ChromosomeExplorer class

The BinnedScatter class

AromaGenomeTextFile

The AromaGenomeTextFile class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

findAnnotationData

Locates an annotation data file

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

The RawCopyNumbers class

estimateSds.CopyNumberChromosomalModel

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

The HaarSegModel class

AromaCellCpgFile

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

getChipType.ChromosomalModel

Gets a label for all chip types merged

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaUnitCallFile

The AromaUnitCallFile class

The UnitTypesFile interface class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaUnitCallSet

The AromaUnitCallSet class

RawCopyNumberModel

The RawCopyNumberModel class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

getPath.AromaTransform

Gets the path of the output data set

aroma.core-package

Package aroma.core

doCBS.character

Performs CBS segmentation on a data set

Applies patches for a specific package

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

getAlias.Explorer

Gets the alias of the output set

The AromaTransform class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

isDone.AromaTransform

Checks if the data set is processed or not

display.Explorer

Displays the explorer in the default browser

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

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaTabularBinaryFile

The AromaTabularBinaryFile class

fit.CopyNumberChromosomalModel

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getFullName.AromaTransform

Gets the full name of the output data set

getNames.ChromosomalModel

Gets the names of the arrays

setAlias.Explorer

Sets the alias of the output set

getName.Explorer

Gets the name of the explorer

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

RawGenomicSignals

The RawGenomicSignals class

nbrOfArrays.Explorer

Gets the total number of arrays

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

fit.CopyNumberSegmentationModel

The AromaPlatform class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

indexOf.UnitNamesFile

Gets the indices of units by their names

getOutputDataSet.AromaTransform

Gets the transformed data set

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

The UnitNamesFile interface class

getTags.AromaTransform

Gets the tags of the output data set

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

RawAlleleBFractions

The RawAlleleBFractions class

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

getInputDataSet.AromaTransform

Gets the input data set

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

writeFooter.AromaTabularBinaryFile

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

segmentByMPCBS.RawGenomicSignals

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

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

nbrOfArrays.ChromosomalModel

Gets the number of arrays

readFooter.AromaTabularBinaryFile

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

getChromosomes.ChromosomalModel

Gets the chromosomes available

RawSequenceReads

The RawSequenceReads class

setArrays.ChromosomeExplorer

Sets the arrays

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

setArrays.Explorer

Sets the arrays

process.AromaTransform

Processes the data set

ChromosomalModel

The ChromosomalModel class

getName.AromaTransform

Gets the name of the output data set

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column