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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
820
Version
3.1.3
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
May 3rd, 2018
Functions in aroma.core (3.1.3)
Search functions
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