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aroma.core (version 3.0.0)
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.packages('aroma.core')
Monthly Downloads
1,036
Version
3.0.0
License
LGPL (>= 2.1)
Issues
2
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0
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1
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Repository
https://github.com/HenrikBengtsson/aroma.core
Homepage
http://www.aroma-project.org/
Maintainer
Henrik Bengtsson
Last Published
January 6th, 2016
Functions in aroma.core (3.0.0)
Search functions
AromaPlatform
The AromaPlatform class
AbstractCNData
The AbstractCNData class
AromaMicroarrayDataSetTuple
The AromaMicroarrayDataSetTuple class
SegmentedGenomicSignalsInterface
The SegmentedGenomicSignalsInterface class interface
getFullName.AromaTransform
Gets the full name of the output data set
process.Explorer
Generates image files, scripts and dynamic pages for the explorer
AromaPlatformInterface
The AromaPlatformInterface class
getChipType.AromaPlatformInterface
Gets the chip type
AromaUnitTotalCnBinarySet
The AromaUnitTotalCnBinarySet class
SegmentedAlleleBFractions
The SegmentedAlleleBFractions class
getModel.ChromosomeExplorer
Gets the model
getChipType.ChromosomalModel
Gets a label for all chip types merged
writeDataFrame.AromaUnitTabularBinaryFile
Writes the data file as a tab-delimited text file
exportAromaUnitPscnBinarySet
Export total and allele B signal data sets as a unified parent-specific copy number signal data set
downloadChipTypeFile.AromaRepository
Download a particular chip type annotation file
downloadFile.AromaRepository
Download a particular file from the reposity
getParameters.ParametersInterface
Gets a list of parameters
fitGenotypeConeBySfit.matrix
Fits an affine transformation to allele A and allele B data
AromaMicroarrayDataFile
The abstract AromaMicroarrayDataFile class
AromaUnitFracBCnBinaryFile
The AromaUnitFracBCnBinaryFile class
AromaUnitTotalCnBinaryFile
The AromaUnitTotalCnBinaryFile class
findFilesTodo.AromaTransform
Finds files in the data set still not processed
Non-documented objects
Non-documented objects
AromaMicroarrayTabularBinaryFile
The AromaMicroarrayTabularBinaryFile class
AromaMicroarrayDataSet
The AromaMicroarrayDataSet class
ChromosomalModel
The ChromosomalModel class
Explorer
The Explorer class
getCacheKey.FileCacheKeyInterface
Gets a list of cache key items
getParametersAsString.ParametersInterface
Gets the parameters as character
nbrOfArrays.Explorer
Gets the total number of arrays
getChromosomes.ChromosomalModel
Gets the chromosomes to be processed
PairedPSCNData
The PairedPSCNData class
AromaUnitFracBCnBinarySet
The AromaUnitFracBCnBinarySet class
AromaCellTabularBinaryFile
The AromaCellTabularBinaryFile class
RawSequenceReads
The RawSequenceReads class
ChromosomeExplorer
The ChromosomeExplorer class
RawMirroredAlleleBFractions
The RawMirroredAlleleBFractions class
ParametersInterface
The ParametersInterface class interface
findAnnotationData
Locates an annotation data file
nbrOfChipTypes.AromaMicroarrayDataSetTuple
Gets the number of chip types
UnitNamesFile
The UnitNamesFile interface class
getAromaPlatform.AromaPlatformInterface
Gets the platform
AbstractPSCNData
The AbstractPSCNData class
getName.AromaTransform
Gets the name of the output data set
AromaUnitCallFile
The AromaUnitCallFile class
CacheKeyInterface
The CacheKeyInterface class interface
BinnedScatter
The BinnedScatter class
indexOf.UnitNamesFile
Gets the indices of units by their names
AromaUnitSignalBinaryFile
The AromaUnitSignalBinaryFile class
getAlias.Explorer
Gets the alias of the output set
getRootPath.AromaTransform
Gets the root path of the output directory
as.GrayscaleImage.matrix
Creates a Grayscale (Color) Image from a matrix file
getCacheKey.CacheKeyInterface
Gets a list of cache key items
readFooter.AromaTabularBinaryFile
Reads the file footer in XML format into a named nested list
CbsModel
The CbsModel class
FileCacheKeyInterface
The FileCacheKeyInterface class interface
process.ChromosomeExplorer
Generates image files, scripts and dynamic pages for the explorer
findAnnotationDataByChipType
Locates an annotation data file by its chip type
segmentByMPCBS.RawGenomicSignals
Segment copy numbers using the multi-platform CBS (mpCBS) method
isDone.AromaTransform
Checks if the data set is processed or not
doCBS
Performs Circular Binary Segmentation (CBS) on a data set
listFiles.AromaRepository
Retrieves the files available on the repository under a particular path
getTags.Explorer
Gets the tags of the explorer
AromaRepository
The AromaRepository class
AromaTabularBinaryFile
The AromaTabularBinaryFile class
colKernelSmoothing.matrix
Kernel smoothing of a matrix column by column
RawAlleleBFractions
The RawAlleleBFractions class
fitMultiDimensionalCone.matrix
Fits an affine transformation to multi-dimensional data
getPath.AromaTransform
Gets the path of the output directory
estimateStandardDeviation.RawGenomicSignals
Estimates the standard deviation of the raw Ys
getChromosomes.ChromosomeExplorer
Gets the chromosomes available
getPath.Explorer
Gets the path of the output directory
getTags.AromaTransform
Gets the tags of the output data set
segmentByHaarSeg.RawGenomicSignals
Segment copy numbers using the HaarSeg method
AromaCellPositionFile
A binary file holding chromosome/position for each cell
getOutputDataSet.AromaTransform
Gets the transformed data set
getRootPath.Explorer
Gets the root path of the output directory
aroma.core-package
Package aroma.core
AromaGenomeTextFile
The AromaGenomeTextFile class
getNames.Explorer
Gets the names of the input samples
AromaUnitCallSet
The AromaUnitCallSet class
matrixBlockPolish.matrix
Applies a polishing function to blocks of rows and columns repeatedly
AromaUnitGenotypeCallFile
The AromaUnitGenotypeCallFile class
process.AromaTransform
Processes the data set
display.Explorer
Displays the explorer in the default browser
AromaUnitTabularBinaryFile
The AromaUnitTabularBinaryFile class
AromaUnitTypesFile
The AromaUnitTypesFile class
RawCopyNumberModel
The RawCopyNumberModel class
estimateSds.CopyNumberChromosomalModel
Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
extractRawCopyNumbers.CopyNumberChromosomalModel
Extracts relative copy numbers
getNames.ChromosomalModel
Gets the names of the arrays
setArrays.Explorer
Sets the arrays
getName.Explorer
Gets the name of the explorer
AromaUnitPscnBinarySet
The AromaUnitPscnBinarySet class
SegmentedCopyNumbers
The SegmentedCopyNumbers class
RawGenomicSignals
The RawGenomicSignals class
AromaTabularBinaryFile$allocate
Creates an AromaTabularBinaryFile
fit.CopyNumberChromosomalModel
Fits the model
nbrOfArrays.ChromosomalModel
Gets the number of arrays
segmentByCBS.RawGenomicSignals
Segment copy numbers using the CBS method
RawCopyNumbers
The RawCopyNumbers class
UnitTypesFile
The UnitTypesFile interface class
colBinnedSmoothing.matrix
Binned smoothing of a matrix column by column
getPlatform.AromaPlatformInterface
Gets the platform
AromaCellCpgFile
A binary file holding local CpG density for each cell (probe/feature)
fitGenotypeCone.matrix
Fits an affine transformation to allele A and allele B data
AromaUnitSignalBinarySet
The AromaUnitSignalBinarySet class
mergeBoxplotStats.list
Merges a list of boxplot.stats() elements
processTime
Gets the running time of the R process and its children processes
writeDataFrame.AromaUnitSignalBinarySet
Writes the data set as a tab-delimited text file
AromaUnitGenotypeCallSet
The AromaUnitGenotypeCallSet class
CopyNumberSegmentationModel
The CopyNumberSegmentationModel class
fit.CopyNumberSegmentationModel
Fits the model
getUnitAnnotationDataFile.AromaPlatformInterface
Gets a unit annotation data file of a particular class
plotTracks.PairedPSCNData
Plots parental specific copy numbers along the genome
segmentByGLAD.RawGenomicSignals
Segment copy numbers using the GLAD method
updateSetupExplorerFile.ChromosomeExplorer
Updates the Javascript file
setArrays.ChromosomeExplorer
Sets the arrays
nbrOfChipTypes.ChromosomalModel
Gets the number of chip types
HaarSegModel
The HaarSegModel class
GladModel
The GladModel class
NonPairedPSCNData
The NonPairedPSCNData class
isCompatibleWith.AromaPlatformInterface
Checks if a particular unit annotation data file is compatible
AromaUnitPscnBinaryFile
The AromaUnitPscnBinaryFile class
getInputDataSet.AromaTransform
Gets the input data set
AromaTransform
The AromaTransform class
writeFooter.AromaTabularBinaryFile
Writes a named nested list to the file footer in XML format
setAlias.Explorer
Sets the alias of the output set
UnitAnnotationDataFile
The UnitAnnotationDataFile interface class
writeDataFrame.AromaUnitSignalBinaryFile
Writes the data file as a tab-delimited text file
AromaTabularBinarySet
The AromaTabularBinarySet class
CopyNumberChromosomalModel
The CopyNumberChromosomalModel class