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aroma.core (version 2.10.0)

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

2.10.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

August 4th, 2013

Functions in aroma.core (2.10.0)

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

getChipType.ChromosomalModel

Gets a label for all chip types merged

estimateSds.CopyNumberChromosomalModel

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

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AbstractPSCNData

The AbstractPSCNData class

Non-documented objects

Non-documented objects

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

CacheKeyInterface

The CacheKeyInterface class interface

AromaCellPositionFile

A binary file holding chromosome/position for each cell

RawCopyNumberModel

The RawCopyNumberModel class

The BinnedScatter class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

AromaUnitCallSet

The AromaUnitCallSet class

isDone.AromaTransform

Checks if the data set is processed or not

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

ChromosomalModel

The ChromosomalModel class

ChromosomeExplorer

The ChromosomeExplorer class

The RawCopyNumbers class

RawAlleleBFractions

The RawAlleleBFractions class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

NonPairedPSCNData

The NonPairedPSCNData class

getCacheKey.CacheKeyInterface

Gets a list of cache key items

AromaUnitCallFile

The AromaUnitCallFile class

The GladModel class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

The AbstractCNData class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

The AromaTransform class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

downloadFile.AromaRepository

Download a particular file from the reposity

findFilesTodo.AromaTransform

Finds files in the data set still not processed

display.Explorer

Displays the explorer in the default browser

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The CbsModel class

findAnnotationData

Locates an annotation data file

Performs Circular Binary Segmentation (CBS) on a data set

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

getParameters.ParametersInterface

Gets a list of parameters

The Explorer class

AromaUnitTypesFile

The AromaUnitTypesFile class

getFullName.AromaTransform

Gets the full name of the output data set

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

AromaCellCpgFile

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

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

indexOf.UnitNamesFile

Gets the indices of units by their names

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

ParametersInterface

The ParametersInterface class interface

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

The HaarSegModel class

getAlias.Explorer

Gets the alias of the output set

downloadPackagePatch

Download a package patch

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

getNames.Explorer

Gets the names of the input samples

AromaRepository

The AromaRepository class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

AromaTabularBinarySet

The AromaTabularBinarySet class

readFooter.AromaTabularBinaryFile

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

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getModel.ChromosomeExplorer

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

aroma.core-package

Package aroma.core

getRootPath.Explorer

Gets the root path of the output directory

setAlias.Explorer

Sets the alias of the output set

getTags.AromaTransform

Gets the tags of the output data set

FileCacheKeyInterface

The FileCacheKeyInterface class interface

The UnitNamesFile interface class

getTags.Explorer

Gets the tags of the explorer

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

fit.CopyNumberSegmentationModel

setArrays.Explorer

Sets the arrays

segmentByMPCBS.RawGenomicSignals

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

The PairedPSCNData class

setArrays.ChromosomeExplorer

Sets the arrays

getName.AromaTransform

Gets the name of the output data set

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

getInputDataSet.AromaTransform

Gets the input data set

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

nbrOfArrays.Explorer

Gets the total number of arrays

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

getOutputDataSet.AromaTransform

Gets the transformed data set

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

getPath.AromaTransform

Gets the path of the output directory

Applies patches for a specific package

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

nbrOfArrays.ChromosomalModel

Gets the number of arrays

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

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

RawSequenceReads

The RawSequenceReads class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getRootPath.AromaTransform

Gets the root path of the output directory

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

process.AromaTransform

Processes the data set

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

RawGenomicSignals

The RawGenomicSignals class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

getName.Explorer

Gets the name of the explorer

getNames.ChromosomalModel

Gets the names of the arrays

The AromaPlatform class

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

getParametersAsString.ParametersInterface

Gets the parameters as character

fit.CopyNumberChromosomalModel

getPath.Explorer

Gets the path of the output directory

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

The UnitTypesFile interface class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

getChromosomes.ChromosomalModel

Gets the chromosomes available