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aroma.core (version 2.14.0)

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

632

Version

2.14.0

License

LGPL (>= 2.1)

Issues

2

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0

Stars

1

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Maintainer

Henrik Bengtsson

Last Published

October 21st, 2015

Functions in aroma.core (2.14.0)

getModel.ChromosomeExplorer

Gets the model
UnitNamesFile

The UnitNamesFile interface class
AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class
AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class
AromaUnitTypesFile

The AromaUnitTypesFile class
RawCopyNumberModel

The RawCopyNumberModel class
NonPairedPSCNData

The NonPairedPSCNData class
AbstractCNData

The AbstractCNData class
AromaUnitCallFile

The AromaUnitCallFile class
colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column
AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class
HaarSegModel

The HaarSegModel class
estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys
CbsModel

The CbsModel class
getChipType.ChromosomalModel

Gets a label for all chip types merged
GladModel

The GladModel class
getInputDataSet.AromaTransform

Gets the input data set
AromaPlatform

The AromaPlatform class
fitGenotypeCone.matrix

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

The AromaPlatformInterface class
fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data
Non-documented objects

Non-documented objects
FileCacheKeyInterface

The FileCacheKeyInterface class interface
setArrays.Explorer

Sets the arrays
findAnnotationDataByChipType

Locates an annotation data file by its chip type
SegmentedCopyNumbers

The SegmentedCopyNumbers class
writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file
AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class
getFullName.AromaTransform

Gets the full name of the output data set
BinnedScatter

The BinnedScatter class
isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible
Explorer

The Explorer class
getRootPath.Explorer

Gets the root path of the output directory
nbrOfChipTypes.ChromosomalModel

Gets the number of chip types
RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class
UnitAnnotationDataFile

The UnitAnnotationDataFile interface class
CopyNumberSegmentationModel

The CopyNumberSegmentationModel class
findAnnotationData

Locates an annotation data file
isDone.AromaTransform

Checks if the data set is processed or not
nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types
extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers
setArrays.ChromosomeExplorer

Sets the arrays
getName.Explorer

Gets the name of the explorer
getChipType.AromaPlatformInterface

Gets the chip type
AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class
ParametersInterface

The ParametersInterface class interface
nbrOfArrays.Explorer

Gets the total number of arrays
segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method
RawAlleleBFractions

The RawAlleleBFractions class
CacheKeyInterface

The CacheKeyInterface class interface
RawCopyNumbers

The RawCopyNumbers class
updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file
as.GrayscaleImage.matrix

Creates a Grayscale (Color) Image from a matrix file
getName.AromaTransform

Gets the name of the output data set
getAlias.Explorer

Gets the alias of the output set
RawGenomicSignals

The RawGenomicSignals class
fit.CopyNumberSegmentationModel

Fits the model
RawSequenceReads

The RawSequenceReads class
process.Explorer

Generates image files, scripts and dynamic pages for the explorer
getPlatform.AromaPlatformInterface

Gets the platform
getPath.Explorer

Gets the path of the output directory
processTime

Gets the running time of the R process and its children processes
indexOf.UnitNamesFile

Gets the indices of units by their names
AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class
estimateSds.CopyNumberChromosomalModel

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

Gets a list of parameters
nbrOfArrays.ChromosomalModel

Gets the number of arrays
AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile
AromaGenomeTextFile

The AromaGenomeTextFile class
AromaRepository

The AromaRepository class
AromaCellCpgFile

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

The AbstractPSCNData class
getChromosomes.ChromosomalModel

Gets the chromosomes to be processed
AromaCellPositionFile

A binary file holding chromosome/position for each cell
AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class
getNames.Explorer

Gets the names of the input samples
AromaTabularBinarySet

The AromaTabularBinarySet class
ChromosomalModel

The ChromosomalModel class
segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class
downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
getCacheKey.CacheKeyInterface

Gets a list of cache key items
AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class
matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly
AromaUnitCallSet

The AromaUnitCallSet class
AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class
CopyNumberChromosomalModel

The CopyNumberChromosomalModel class
colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column
downloadFile.AromaRepository

Download a particular file from the reposity
SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface
getCacheKey.FileCacheKeyInterface

Gets a list of cache key items
segmentByMPCBS.RawGenomicSignals

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

Fits the model
getTags.AromaTransform

Gets the tags of the output data set
AromaMicroarrayDataSet

The AromaMicroarrayDataSet class
aroma.core-package

Package aroma.core
ChromosomeExplorer

The ChromosomeExplorer class
display.Explorer

Displays the explorer in the default browser
getRootPath.AromaTransform

Gets the root path of the output directory
listFiles.AromaRepository

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

The AromaCellTabularBinaryFile class
AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class
AromaTabularBinaryFile

The AromaTabularBinaryFile class
AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class
PairedPSCNData

The PairedPSCNData class
UnitTypesFile

The UnitTypesFile interface class
fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data
findFilesTodo.AromaTransform

Finds files in the data set still not processed
getPath.AromaTransform

Gets the path of the output directory
AromaTransform

The AromaTransform class
process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer
process.AromaTransform

Processes the data set
doCBS

Performs Circular Binary Segmentation (CBS) on a data set
AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class
getOutputDataSet.AromaTransform

Gets the transformed data set
getParametersAsString.ParametersInterface

Gets the parameters as character
getChromosomes.ChromosomeExplorer

Gets the chromosomes available
setAlias.Explorer

Sets the alias of the output set
getTags.Explorer

Gets the tags of the explorer
readFooter.AromaTabularBinaryFile

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

Segment copy numbers using the CBS method
exportAromaUnitPscnBinarySet

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

Gets the platform
getNames.ChromosomalModel

Gets the names of the arrays
writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file
plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome