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aroma.core (version 3.1.3)

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

588

Version

3.1.3

License

LGPL (>= 2.1)

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Pull Requests

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Repository

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

Homepage

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

Maintainer

Henrik Bengtsson

Last Published

May 3rd, 2018

Functions in aroma.core (3.1.3)

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

The HaarSegModel class

AromaPlatformInterface

The AromaPlatformInterface class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

ChromosomeExplorer

The ChromosomeExplorer class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

NonPairedPSCNData

The NonPairedPSCNData class

The PairedPSCNData class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

estimateSds.CopyNumberChromosomalModel

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

ChromosomalModel

The ChromosomalModel class

The CbsModel class

Non-documented objects

Non-documented objects

The UnitNamesFile interface class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class

The BinnedScatter class

AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class

findFilesTodo.AromaTransform

Finds files in the data set still not processed

RawCopyNumberModel

The RawCopyNumberModel class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The GladModel class

AromaUnitTypesFile

The AromaUnitTypesFile class

CacheKeyInterface

The CacheKeyInterface class interface

fit.CopyNumberChromosomalModel

RawSequenceReads

The RawSequenceReads class

The RawCopyNumbers class

FileCacheKeyInterface

The FileCacheKeyInterface class interface

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

The UnitTypesFile interface class

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile

findAnnotationData

Locates an annotation data file

exportAromaUnitPscnBinarySet

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

getChipType.AromaPlatformInterface

Gets the chip type

RawGenomicSignals

The RawGenomicSignals class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

getChipType.ChromosomalModel

Gets a label for all chip types merged

display.Explorer

Displays the explorer in the default browser

Performs Circular Binary Segmentation (CBS) on a data set

getInputDataSet.AromaTransform

Gets the input data set

getFullName.AromaTransform

Gets the full name of the output data set

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getNames.Explorer

Gets the names of the input samples

The Explorer class

getPlatform.AromaPlatformInterface

Gets the platform

getRootPath.AromaTransform

Gets the root path of the output directory

aroma.core-package

Package aroma.core

getModel.ChromosomeExplorer

getRootPath.Explorer

Gets the root path of the output directory

as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file

getOutputDataSet.AromaTransform

Gets the transformed data set

downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file

getTags.AromaTransform

Gets the tags of the output data set

ParametersInterface

The ParametersInterface class interface

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getTags.Explorer

Gets the tags of the explorer

RawAlleleBFractions

The RawAlleleBFractions class

getName.AromaTransform

Gets the name of the output data set

getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class

plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

process.AromaTransform

Processes the data set

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

setArrays.Explorer

Sets the arrays

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getParameters.ParametersInterface

Gets a list of parameters

downloadFile.AromaRepository

Download a particular file from the reposity

getAlias.Explorer

Gets the alias of the output set

updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file

getParametersAsString.ParametersInterface

Gets the parameters as character

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

indexOf.UnitNamesFile

Gets the indices of units by their names

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible

fit.CopyNumberSegmentationModel

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

getCacheKey.CacheKeyInterface

Gets a list of cache key items

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

getCacheKey.FileCacheKeyInterface

Gets a list of cache key items

getName.Explorer

Gets the name of the explorer

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

segmentByMPCBS.RawGenomicSignals

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

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getNames.ChromosomalModel

Gets the names of the arrays

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

getAromaPlatform.AromaPlatformInterface

Gets the platform

getChromosomes.ChromosomalModel

Gets the chromosomes to be processed

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

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getPath.Explorer

Gets the path of the output directory

writeFooter.AromaTabularBinaryFile

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

isDone.AromaTransform

Checks if the data set is processed or not

getPath.AromaTransform

Gets the path of the output directory

readFooter.AromaTabularBinaryFile

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

listFiles.AromaRepository

Retrieves the files available on the repository under a particular path

nbrOfArrays.ChromosomalModel

Gets the number of arrays

nbrOfArrays.Explorer

Gets the total number of arrays

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

setAlias.Explorer

Sets the alias of the output set

setArrays.ChromosomeExplorer

Sets the arrays

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AbstractCNData class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaCellCpgFile

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

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AbstractPSCNData

The AbstractPSCNData class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

AromaTabularBinarySet

The AromaTabularBinarySet class

The AromaTransform class

The AromaPlatform class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitCallFile

The AromaUnitCallFile class

AromaRepository

The AromaRepository class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class