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aroma.core (version 2.2.0)

Core methods and classes used by aroma.* package part of The Aroma Project

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

731

Version

2.2.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

September 3rd, 2011

Functions in aroma.core (2.2.0)

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class
AromaTabularBinarySet

The AromaTabularBinarySet class
AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class
colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column
ChromosomalModel

The ChromosomalModel class
CopyNumberChromosomalModel

The CopyNumberChromosomalModel class
RawCopyNumberModel

The RawCopyNumberModel class
RawGenomicSignals

The RawGenomicSignals class
AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class
CbsModel

The CbsModel class
fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data
setArrays.Explorer

Sets the arrays
SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface
estimateSds.CopyNumberChromosomalModel

Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
getNames.Explorer

Gets the names of the input samples
downloadPackagePatch

Download a package patch
findAnnotationDataByChipType

Locates an annotation data file by its chip type
getAlias.Explorer

Gets the alias of the output set
RawAlleleBFractions

The RawAlleleBFractions class
getTags.AromaTransform

Gets the tags of the output data set
getNames.ChromosomalModel

Gets the names of the arrays
AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class
getPath.AromaTransform

Gets the path of the output data set
process.Explorer

Generates image files, scripts and dynamic pages for the explorer
as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file
isDone.AromaTransform

Checks if the data set is processed or not
getModel.ChromosomeExplorer

Gets the model
getChipType.ChromosomalModel

Gets a label for all chip types merged
getName.Explorer

Gets the name of the explorer
processTime

Gets the running time of the R process and its children processes
nbrOfChipTypes.ChromosomalModel

Gets the number of chip types
AromaTabularBinaryFile

The AromaTabularBinaryFile class
updateSamplesFile.ChromosomeExplorer

Updates the samples.js file
segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method
RawCopyNumbers

The RawCopyNumbers class
mergeBoxplotStats.list

Merges a list of boxplot.stats() elements
nbrOfArrays.Explorer

Gets the total number of arrays
findAnnotationData

Locates an annotation data file
getChromosomes.ChromosomalModel

Gets the chromosomes available
RawSequenceReads

The RawSequenceReads class
getTags.Explorer

Gets the tags of the explorer
writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file
getOutputDataSet.AromaTransform

Gets the transformed data set
AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class
fit.CopyNumberChromosomalModel

Fits the model
indexOf.UnitNamesFile

Gets the indices of units by their names
getFullName.AromaTransform

Gets the full name of the output data set
CopyNumberSegmentationModel

The CopyNumberSegmentationModel class
segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method
AromaPlatform

The AromaPlatform class
writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file
GladModel

The GladModel class
fit.CopyNumberSegmentationModel

Fits the model
AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class
AromaCellCpgFile

A binary file holding local CpG density for each cell (probe/feature)
Explorer

The Explorer class
UnitTypesFile

The UnitTypesFile interface class
AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class
segmentByMPCBS.RawGenomicSignals

Segment copy numbers using the multi-platform CBS (mpCBS) method
allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile
fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data
nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types
setArrays.ChromosomeExplorer

Sets the arrays
nbrOfArrays.ChromosomalModel

Gets the number of arrays
AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class
ChromosomeExplorer

The ChromosomeExplorer class
getInputDataSet.AromaTransform

Gets the input data set
matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly
AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class
UnitAnnotationDataFile

The UnitAnnotationDataFile interface class
colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column
doCBS.character

Performs CBS segmentation on a data set
writeFooter.AromaTabularBinaryFile

Writes a named nested list to the file footer in XML format
AromaTransform

The AromaTransform class
AromaUnitCallFile

The AromaUnitCallFile class
BinnedScatter

The BinnedScatter class
HaarSegModel

The HaarSegModel class
SegmentedAlleleBFractions

The SegmentedAlleleBFractions class
extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers
writeDataFrame.AromaUnitSignalBinaryFile

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

A binary file holding chromosome/position for each cell
AromaGenomeTextFile

The AromaGenomeTextFile class
UnitNamesFile

The UnitNamesFile interface class
display.Explorer

Displays the explorer in the default browser
AromaMicroarrayDataSet

The AromaMicroarrayDataSet class
AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class
AromaUnitTypesFile

The AromaUnitTypesFile class
AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class
Non-documented objects

Non-documented objects
process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer
setAlias.Explorer

Sets the alias of the output set
AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class
RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class
SegmentedCopyNumbers

The SegmentedCopyNumbers class
patchPackage

Applies patches for a specific package
readFooter.AromaTabularBinaryFile

Reads the file footer in XML format into a named nested list
process.AromaTransform

Processes the data set
AromaUnitCallSet

The AromaUnitCallSet class
AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class
aroma.core-package

Package aroma.core
estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys
getChromosomes.ChromosomeExplorer

Gets the chromosomes available
fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data
segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method
getName.AromaTransform

Gets the name of the output data set