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aroma.core (version 3.1.1)

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.packages('aroma.core')

Monthly Downloads

731

Version

3.1.1

License

LGPL (>= 2.1)

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Maintainer

Henrik Bengtsson

Last Published

September 13th, 2017

Functions in aroma.core (3.1.1)

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class
AromaGenomeTextFile

The AromaGenomeTextFile class
AbstractCNData

The AbstractCNData class
AbstractPSCNData

The AbstractPSCNData class
AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class
AromaMicroarrayDataSet

The AromaMicroarrayDataSet class
AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class
AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class
AromaCellCpgFile

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

A binary file holding chromosome/position for each cell
AromaPlatform

The AromaPlatform class
AromaPlatformInterface

The AromaPlatformInterface class
AromaTabularBinarySet

The AromaTabularBinarySet class
AromaTransform

The AromaTransform class
AromaRepository

The AromaRepository class
AromaTabularBinaryFile

The AromaTabularBinaryFile class
AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class
AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class
AromaUnitCallFile

The AromaUnitCallFile class
AromaUnitCallSet

The AromaUnitCallSet class
AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class
AromaUnitTypesFile

The AromaUnitTypesFile class
BinnedScatter

The BinnedScatter class
CacheKeyInterface

The CacheKeyInterface class interface
NonPairedPSCNData

The NonPairedPSCNData class
AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class
AromaUnitPscnBinarySet

The AromaUnitPscnBinarySet class
FileCacheKeyInterface

The FileCacheKeyInterface class interface
GladModel

The GladModel class
PairedPSCNData

The PairedPSCNData class
UnitAnnotationDataFile

The UnitAnnotationDataFile interface class
UnitNamesFile

The UnitNamesFile interface class
RawCopyNumberModel

The RawCopyNumberModel class
RawCopyNumbers

The RawCopyNumbers class
aroma.core-package

Package aroma.core
as.GrayscaleImage.matrix

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

The CopyNumberSegmentationModel class
Explorer

The Explorer class
RawGenomicSignals

The RawGenomicSignals class
AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class
AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class
CbsModel

The CbsModel class
colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column
colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column
findAnnotationData

Locates an annotation data file
findAnnotationDataByChipType

Locates an annotation data file by its chip type
getChipType.AromaPlatformInterface

Gets the chip type
ChromosomeExplorer

The ChromosomeExplorer class
CopyNumberChromosomalModel

The CopyNumberChromosomalModel class
HaarSegModel

The HaarSegModel class
Non-documented objects

Non-documented objects
SegmentedCopyNumbers

The SegmentedCopyNumbers class
SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface
exportAromaUnitPscnBinarySet

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

Extracts relative copy numbers
fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data
fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data
getChromosomes.ChromosomalModel

Gets the chromosomes to be processed
ChromosomalModel

The ChromosomalModel class
ParametersInterface

The ParametersInterface class interface
RawAlleleBFractions

The RawAlleleBFractions class
UnitTypesFile

The UnitTypesFile interface class
AromaTabularBinaryFile$allocate

Creates an AromaTabularBinaryFile
downloadChipTypeFile.AromaRepository

Download a particular chip type annotation file
downloadFile.AromaRepository

Download a particular file from the reposity
getChipType.ChromosomalModel

Gets a label for all chip types merged
getPath.AromaTransform

Gets the path of the output directory
getPath.Explorer

Gets the path of the output directory
indexOf.UnitNamesFile

Gets the indices of units by their names
isCompatibleWith.AromaPlatformInterface

Checks if a particular unit annotation data file is compatible
RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class
getChromosomes.ChromosomeExplorer

Gets the chromosomes available
getNames.Explorer

Gets the names of the input samples
getOutputDataSet.AromaTransform

Gets the transformed data set
isDone.AromaTransform

Checks if the data set is processed or not
listFiles.AromaRepository

Retrieves the files available on the repository under a particular path
process.ChromosomeExplorer

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

Generates image files, scripts and dynamic pages for the explorer
setArrays.Explorer

Sets the arrays
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
writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file
display.Explorer

Displays the explorer in the default browser
doCBS

Performs Circular Binary Segmentation (CBS) on a data set
fit.CopyNumberSegmentationModel

Fits the model
fitGenotypeCone.matrix

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

Gets the full name of the output data set
getInputDataSet.AromaTransform

Gets the input data set
getPlatform.AromaPlatformInterface

Gets the platform
getRootPath.AromaTransform

Gets the root path of the output directory
findFilesTodo.AromaTransform

Finds files in the data set still not processed
fit.CopyNumberChromosomalModel

Fits the model
getCacheKey.CacheKeyInterface

Gets a list of cache key items
matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly
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
updateSetupExplorerFile.ChromosomeExplorer

Updates the Javascript file
RawSequenceReads

The RawSequenceReads class
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
estimateSds.CopyNumberChromosomalModel

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

Estimates the standard deviation of the raw Ys
getCacheKey.FileCacheKeyInterface

Gets a list of cache key items
getParameters.ParametersInterface

Gets a list of parameters
getParametersAsString.ParametersInterface

Gets the parameters as character
getTags.Explorer

Gets the tags of the explorer
getUnitAnnotationDataFile.AromaPlatformInterface

Gets a unit annotation data file of a particular class
segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method
segmentByMPCBS.RawGenomicSignals

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

Gets the alias of the output set
getAromaPlatform.AromaPlatformInterface

Gets the platform
getModel.ChromosomeExplorer

Gets the model
getName.AromaTransform

Gets the name of the output data set
getName.Explorer

Gets the name of the explorer
plotTracks.PairedPSCNData

Plots parental specific copy numbers along the genome
process.AromaTransform

Processes the data set
segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method
getNames.ChromosomalModel

Gets the names of the arrays
getRootPath.Explorer

Gets the root path of the output directory
getTags.AromaTransform

Gets the tags of the output data set
processTime

Gets the running time of the R process and its children processes
readFooter.AromaTabularBinaryFile

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

Segment copy numbers using the GLAD method
setAlias.Explorer

Sets the alias of the output set
setArrays.ChromosomeExplorer

Sets the arrays
writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file
writeFooter.AromaTabularBinaryFile

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