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aroma.core (version 2.2.2)

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

2.2.2

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

October 19th, 2011

Functions in aroma.core (2.2.2)

getChipType.ChromosomalModel

Gets a label for all chip types merged

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

getModel.ChromosomeExplorer

RawAlleleBFractions

The RawAlleleBFractions class

findAnnotationData

Locates an annotation data file

setAlias.Explorer

Sets the alias of the output set

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

The BinnedScatter class

getNames.Explorer

Gets the names of the input samples

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

getOutputDataSet.AromaTransform

Gets the transformed data set

nbrOfArrays.Explorer

Gets the total number of arrays

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaCellCpgFile

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

getTags.Explorer

Gets the tags of the explorer

The RawCopyNumbers class

AromaTabularBinarySet

The AromaTabularBinarySet class

getNames.ChromosomalModel

Gets the names of the arrays

Non-documented objects

Non-documented objects

aroma.core-package

Package aroma.core

The GladModel class

The UnitNamesFile interface class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

The UnitTypesFile interface class

The CbsModel class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

isDone.AromaTransform

Checks if the data set is processed or not

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

estimateSds.CopyNumberChromosomalModel

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

downloadPackagePatch

Download a package patch

findAnnotationDataByChipType

Locates an annotation data file by its chip type

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The AromaPlatform class

readFooter.AromaTabularBinaryFile

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

getFullName.AromaTransform

Gets the full name of the output data set

setArrays.Explorer

Sets the arrays

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

writeFooter.AromaTabularBinaryFile

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

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitTypesFile

The AromaUnitTypesFile class

getInputDataSet.AromaTransform

Gets the input data set

nbrOfArrays.ChromosomalModel

Gets the number of arrays

doCBS.character

Performs CBS segmentation on a data set

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaUnitCallSet

The AromaUnitCallSet class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

The Explorer class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

AromaTabularBinaryFile

The AromaTabularBinaryFile class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

The HaarSegModel class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

display.Explorer

Displays the explorer in the default browser

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getChromosomes.ChromosomalModel

Gets the chromosomes available

RawGenomicSignals

The RawGenomicSignals class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

getName.AromaTransform

Gets the name of the output data set

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

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

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

RawSequenceReads

The RawSequenceReads class

fit.CopyNumberSegmentationModel

The AromaTransform class

getTags.AromaTransform

Gets the tags of the output data set

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getName.Explorer

Gets the name of the explorer

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

segmentByMPCBS.RawGenomicSignals

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

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

ChromosomeExplorer

The ChromosomeExplorer class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

fit.CopyNumberChromosomalModel

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

RawCopyNumberModel

The RawCopyNumberModel class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

ChromosomalModel

The ChromosomalModel class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getPath.AromaTransform

Gets the path of the output data set

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

getAlias.Explorer

Gets the alias of the output set

process.AromaTransform

Processes the data set

Applies patches for a specific package

setArrays.ChromosomeExplorer

Sets the arrays

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types