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aroma.core (version 3.1.2)

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Description

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

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Install

install.packages('aroma.core')

Monthly Downloads

589

Version

3.1.2

License

LGPL (>= 2.1)

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Repository

https://github.com/HenrikBengtsson/aroma.core

Homepage

http://www.aroma-project.org/

Maintainer

Henrik Bengtsson

Last Published

April 24th, 2018

Functions in aroma.core (3.1.2)

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

RawCopyNumberModel

The RawCopyNumberModel class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

The Explorer class

The UnitTypesFile interface class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

The RawCopyNumbers class

exportAromaUnitPscnBinarySet

Export total and allele B signal data sets as a unified parent-specific copy number signal data set

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

estimateSds.CopyNumberChromosomalModel

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

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

NonPairedPSCNData

The NonPairedPSCNData class

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The PairedPSCNData class

ChromosomeExplorer

The ChromosomeExplorer class

The GladModel class

AromaTabularBinarySet

The AromaTabularBinarySet class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

Performs Circular Binary Segmentation (CBS) on a data set

RawGenomicSignals

The RawGenomicSignals class

The HaarSegModel class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The BinnedScatter class

CacheKeyInterface

The CacheKeyInterface class interface

The AromaTransform class

aroma.core-package

Package aroma.core

The UnitNamesFile interface class

fit.CopyNumberSegmentationModel

display.Explorer

Displays the explorer in the default browser

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

Non-documented objects

Non-documented objects

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

The CbsModel class

ParametersInterface

The ParametersInterface class interface

RawSequenceReads

The RawSequenceReads class

ChromosomalModel

The ChromosomalModel class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

downloadFile.AromaRepository

Download a particular file from the reposity

RawAlleleBFractions

The RawAlleleBFractions class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

getTags.Explorer

Gets the tags of the explorer

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

getParametersAsString.ParametersInterface

Gets the parameters as character

getAromaPlatform.AromaPlatformInterface

Gets the platform

getFullName.AromaTransform

Gets the full name of the output data set

getInputDataSet.AromaTransform

Gets the input data set

getParameters.ParametersInterface

Gets a list of parameters

getAlias.Explorer

Gets the alias of the output set

getChipType.AromaPlatformInterface

Gets the chip type

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

findAnnotationData

Locates an annotation data file

findAnnotationDataByChipType

Locates an annotation data file by its chip type

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfArrays.Explorer

Gets the total number of arrays

getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class

getChipType.ChromosomalModel

Gets a label for all chip types merged

fit.CopyNumberChromosomalModel

findFilesTodo.AromaTransform

Finds files in the data set still not processed

getName.Explorer

Gets the name of the explorer

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getModel.ChromosomeExplorer

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

indexOf.UnitNamesFile

Gets the indices of units by their names

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

segmentByMPCBS.RawGenomicSignals

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

getNames.ChromosomalModel

Gets the names of the arrays

getName.AromaTransform

Gets the name of the output data set

getNames.Explorer

Gets the names of the input samples

getOutputDataSet.AromaTransform

Gets the transformed data set

writeFooter.AromaTabularBinaryFile

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

getCacheKey.CacheKeyInterface

Gets a list of cache key items

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

getPath.AromaTransform

Gets the path of the output directory

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getPath.Explorer

Gets the path of the output directory

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

getRootPath.Explorer

Gets the root path of the output directory

getRootPath.AromaTransform

Gets the root path of the output directory

getPlatform.AromaPlatformInterface

Gets the platform

getTags.AromaTransform

Gets the tags of the output data set

isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

isDone.AromaTransform

Checks if the data set is processed or not

process.AromaTransform

Processes the data set

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

setAlias.Explorer

Sets the alias of the output set

readFooter.AromaTabularBinaryFile

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

setArrays.ChromosomeExplorer

Sets the arrays

setArrays.Explorer

Sets the arrays

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

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AbstractCNData class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AbstractPSCNData

The AbstractPSCNData class

AromaCellCpgFile

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

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitCallSet

The AromaUnitCallSet class

AromaPlatformInterface

The AromaPlatformInterface class

The AromaPlatform class

AromaRepository

The AromaRepository class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class