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aroma.core (version 2.3.2)

Core methods and classes used by aroma.* packages part of The Aroma Framework

Description

This package contains core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn. Its API should be considered to be in alpha and beta versions, and is mostly of interest to developers.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

2.3.2

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

November 15th, 2011

Functions in aroma.core (2.3.2)

AromaCellPositionFile

A binary file holding chromosome/position for each cell
mergeBoxplotStats.list

Merges a list of boxplot.stats() elements
AromaTabularBinaryFile

The AromaTabularBinaryFile class
getOutputDataSet.AromaTransform

Gets the transformed data set
CopyNumberSegmentationModel

The CopyNumberSegmentationModel class
getName.Explorer

Gets the name of the explorer
getFullName.AromaTransform

Gets the full name of the output data set
AromaGenomeTextFile

The AromaGenomeTextFile class
segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method
extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers
patchPackage

Applies patches for a specific package
getName.AromaTransform

Gets the name of the output data set
GladModel

The GladModel class
setArrays.Explorer

Sets the arrays
AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class
estimateSds.CopyNumberChromosomalModel

Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
CopyNumberChromosomalModel

The CopyNumberChromosomalModel class
ChromosomeExplorer

The ChromosomeExplorer class
UnitTypesFile

The UnitTypesFile interface class
RawGenomicSignals

The RawGenomicSignals class
process.AromaTransform

Processes the data set
findAnnotationData

Locates an annotation data file
getNames.Explorer

Gets the names of the input samples
RawCopyNumbers

The RawCopyNumbers class
AromaTransform

The AromaTransform class
matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly
readFooter.AromaTabularBinaryFile

Reads the file footer in XML format into a named nested list
nbrOfArrays.Explorer

Gets the total number of arrays
updateSamplesFile.ChromosomeExplorer

Updates the samples.js file
AromaMicroarrayDataSet

The AromaMicroarrayDataSet class
getChromosomes.ChromosomeExplorer

Gets the chromosomes available
AromaPlatform

The AromaPlatform class
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class
UnitAnnotationDataFile

The UnitAnnotationDataFile interface class
getAlias.Explorer

Gets the alias of the output set
setAlias.Explorer

Sets the alias of the output set
getChipType.ChromosomalModel

Gets a label for all chip types merged
segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method
segmentByMPCBS.RawGenomicSignals

Segment copy numbers using the multi-platform CBS (mpCBS) method
AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class
AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class
display.Explorer

Displays the explorer in the default browser
AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class
processTime

Gets the running time of the R process and its children processes
writeFooter.AromaTabularBinaryFile

Writes a named nested list to the file footer in XML format
fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data
colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column
AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class
AromaUnitCallFile

The AromaUnitCallFile class
isDone.AromaTransform

Checks if the data set is processed or not
Explorer

The Explorer class
SegmentedCopyNumbers

The SegmentedCopyNumbers class
UnitNamesFile

The UnitNamesFile interface class
CbsModel

The CbsModel class
AromaUnitTypesFile

The AromaUnitTypesFile class
fit.CopyNumberChromosomalModel

Fits the model
getTags.Explorer

Gets the tags of the explorer
RawSequenceReads

The RawSequenceReads class
fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data
RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class
downloadPackagePatch

Download a package patch
nbrOfChipTypes.ChromosomalModel

Gets the number of chip types
getModel.ChromosomeExplorer

Gets the model
getTags.AromaTransform

Gets the tags of the output data set
nbrOfArrays.ChromosomalModel

Gets the number of arrays
SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface
fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data
writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file
process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer
RawCopyNumberModel

The RawCopyNumberModel class
getInputDataSet.AromaTransform

Gets the input data set
getNames.ChromosomalModel

Gets the names of the arrays
findAnnotationDataByChipType

Locates an annotation data file by its chip type
Non-documented objects

Non-documented objects
AromaTabularBinarySet

The AromaTabularBinarySet class
writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file
AromaCellCpgFile

A binary file holding local CpG density for each cell (probe/feature)
estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys
colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column
nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile
getChromosomes.ChromosomalModel

Gets the chromosomes available
AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class
AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class
indexOf.UnitNamesFile

Gets the indices of units by their names
fit.CopyNumberSegmentationModel

Fits the model
AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class
as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file
setArrays.ChromosomeExplorer

Sets the arrays
HaarSegModel

The HaarSegModel class
AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class
ChromosomalModel

The ChromosomalModel class
aroma.core-package

Package aroma.core
getPath.AromaTransform

Gets the path of the output data set
writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file
process.Explorer

Generates image files, scripts and dynamic pages for the explorer
segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method
AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class
BinnedScatter

The BinnedScatter class
AromaUnitCallSet

The AromaUnitCallSet class
RawAlleleBFractions

The RawAlleleBFractions class
doCBS.character

Performs CBS segmentation on a data set