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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
820
Version
3.1.1
License
LGPL (>= 2.1)
Issues
2
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0
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Repository
https://github.com/HenrikBengtsson/aroma.core
Homepage
http://www.aroma-project.org/
Maintainer
Henrik Bengtsson
Last Published
September 13th, 2017
Functions in aroma.core (3.1.1)
Search functions
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