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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.packages('aroma.core')

Monthly Downloads

588

Version

3.1.3

License

LGPL (>= 2.1)

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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
HaarSegModel

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
PairedPSCNData

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
CbsModel

The CbsModel class
Non-documented objects

Non-documented objects
UnitNamesFile

The UnitNamesFile interface class
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys
AromaUnitPscnBinaryFile

The AromaUnitPscnBinaryFile class
BinnedScatter

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
GladModel

The GladModel class
AromaUnitTypesFile

The AromaUnitTypesFile class
CacheKeyInterface

The CacheKeyInterface class interface
fit.CopyNumberChromosomalModel

Fits the model
RawSequenceReads

The RawSequenceReads class
RawCopyNumbers

The RawCopyNumbers class
FileCacheKeyInterface

The FileCacheKeyInterface class interface
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
UnitTypesFile

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
doCBS

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
Explorer

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

Gets the model
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

Fits the model
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
processTime

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
AbstractCNData

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
AromaTransform

The AromaTransform class
AromaPlatform

The AromaPlatform class
AromaTabularBinaryFile

The AromaTabularBinaryFile class
AromaUnitCallFile

The AromaUnitCallFile class
AromaRepository

The AromaRepository class
AromaGenomeTextFile

The AromaGenomeTextFile class
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class