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aroma.core (version 2.13.1)

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

2.13.1

License

LGPL (>= 2.1)

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2

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0

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1

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Maintainer

Henrik Bengtsson

Last Published

May 26th, 2015

Functions in aroma.core (2.13.1)

CacheKeyInterface

The CacheKeyInterface class interface
mergeBoxplotStats.list

Merges a list of boxplot.stats() elements
AromaUnitCallSet

The AromaUnitCallSet class
FileCacheKeyInterface

The FileCacheKeyInterface class interface
AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class
AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class
AromaTabularBinarySet

The AromaTabularBinarySet class
RawCopyNumbers

The RawCopyNumbers class
AromaUnitTypesFile

The AromaUnitTypesFile class
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
listFiles.AromaRepository

Retrieves the files available on the repository under a particular path
CbsModel

The CbsModel class
AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class
AromaTabularBinaryFile

The AromaTabularBinaryFile class
AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class
AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class
colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column
display.Explorer

Displays the explorer in the default browser
fit.CopyNumberSegmentationModel

Fits the model
AbstractPSCNData

The AbstractPSCNData class
RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class
CopyNumberSegmentationModel

The CopyNumberSegmentationModel class
AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class
AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class
AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class
extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers
AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class
exportAromaUnitPscnBinarySet

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

Gets the model
AromaPlatformInterface

The AromaPlatformInterface class
ChromosomeExplorer

The ChromosomeExplorer class
as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file
AromaUnitCallFile

The AromaUnitCallFile class
aroma.core-package

Package aroma.core
CopyNumberChromosomalModel

The CopyNumberChromosomalModel class
getChipType.ChromosomalModel

Gets a label for all chip types merged
SegmentedCopyNumbers

The SegmentedCopyNumbers class
getPath.Explorer

Gets the path of the output directory
AromaPlatform

The AromaPlatform class
downloadFile.AromaRepository

Download a particular file from the reposity
getChipType.AromaPlatformInterface

Gets the chip type
AromaTransform

The AromaTransform class
downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file
getName.Explorer

Gets the name of the explorer
AromaCellCpgFile

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

The UnitTypesFile interface class
getPlatform.AromaPlatformInterface

Gets the platform
AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile
estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys
Explorer

The Explorer class
segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method
nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface
UnitNamesFile

The UnitNamesFile interface class
setArrays.Explorer

Sets the arrays
nbrOfArrays.ChromosomalModel

Gets the number of arrays
process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer
GladModel

The GladModel class
getCacheKey.CacheKeyInterface

Gets a list of cache key items
AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class
getRootPath.AromaTransform

Gets the root path of the output directory
AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class
getNames.ChromosomalModel

Gets the names of the arrays
AromaCellPositionFile

A binary file holding chromosome/position for each cell
Non-documented objects

Non-documented objects
getTags.Explorer

Gets the tags of the explorer
isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible
writeFooter.AromaTabularBinaryFile

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

The ParametersInterface class interface
nbrOfArrays.Explorer

Gets the total number of arrays
matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly
colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column
updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file
writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file
fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data
plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome
readFooter.AromaTabularBinaryFile

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

Gets the number of chip types
findFilesTodo.AromaTransform

Finds files in the data set still not processed
segmentByMPCBS.RawGenomicSignals

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

Fits the model
AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class
RawAlleleBFractions

The RawAlleleBFractions class
getParametersAsString.ParametersInterface

Gets the parameters as character
fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data
processTime

Gets the running time of the R process and its children processes
getNames.Explorer

Gets the names of the input samples
getOutputDataSet.AromaTransform

Gets the transformed data set
process.AromaTransform

Processes the data set
RawGenomicSignals

The RawGenomicSignals class
getChromosomes.ChromosomeExplorer

Gets the chromosomes available
setAlias.Explorer

Sets the alias of the output set
getInputDataSet.AromaTransform

Gets the input data set
BinnedScatter

The BinnedScatter class
estimateSds.CopyNumberChromosomalModel

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

Gets the full name of the output data set
getParameters.ParametersInterface

Gets a list of parameters
findAnnotationData

Locates an annotation data file
segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method
isDone.AromaTransform

Checks if the data set is processed or not
getPath.AromaTransform

Gets the path of the output directory
PairedPSCNData

The PairedPSCNData class
process.Explorer

Generates image files, scripts and dynamic pages for the explorer
findAnnotationDataByChipType

Locates an annotation data file by its chip type
indexOf.UnitNamesFile

Gets the indices of units by their names
setArrays.ChromosomeExplorer

Sets the arrays
getRootPath.Explorer

Gets the root path of the output directory
AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class
segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method
RawSequenceReads

The RawSequenceReads class
fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data
UnitAnnotationDataFile

The UnitAnnotationDataFile interface class
getAromaPlatform.AromaPlatformInterface

Gets the platform
writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file
getName.AromaTransform

Gets the name of the output data set
AromaMicroarrayDataSet

The AromaMicroarrayDataSet class
AromaGenomeTextFile

The AromaGenomeTextFile class
NonPairedPSCNData

The NonPairedPSCNData class
getTags.AromaTransform

Gets the tags of the output data set
AbstractCNData

The AbstractCNData class
AromaRepository

The AromaRepository class
ChromosomalModel

The ChromosomalModel class
RawCopyNumberModel

The RawCopyNumberModel class
HaarSegModel

The HaarSegModel class
getAlias.Explorer

Gets the alias of the output set
getChromosomes.ChromosomalModel

Gets the chromosomes to be processed
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class
doCBS

Performs Circular Binary Segmentation (CBS) on a data set
getCacheKey.FileCacheKeyInterface

Gets a list of cache key items
getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class
writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file