Learn R Programming
⚠️There's a newer version (3.3.2) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

3.0.0

License

LGPL (>= 2.1)

Issues

2

Pull Requests

0

Stars

1

Forks

1

Maintainer

Henrik Bengtsson

Last Published

January 6th, 2016

Functions in aroma.core (3.0.0)

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