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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
1,036
Version
2.14.0
License
LGPL (>= 2.1)
Issues
2
Pull Requests
0
Stars
1
Forks
1
Repository
https://github.com/HenrikBengtsson/aroma.core
Homepage
http://www.aroma-project.org/
Maintainer
Henrik Bengtsson
Last Published
October 21st, 2015
Functions in aroma.core (2.14.0)
Search functions
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