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aroma.core (version 1.9.1)

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

588

Version

1.9.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

January 15th, 2011

Functions in aroma.core (1.9.1)

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getFullName.AromaTransform

Gets the full name of the output data set

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaUnitCallSet

The AromaUnitCallSet class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

getNames.Explorer

Gets the names of the input samples

AromaUnitCallFile

The AromaUnitCallFile class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

RawCopyNumberModel

The RawCopyNumberModel class

The AromaTransform class

The UnitTypesFile interface class

RawSequenceReads

The RawSequenceReads class

Non-documented objects

Non-documented objects

The GladModel class

downloadPackagePatch

Download a package patch

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

indexOf.UnitNamesFile

Gets the indices of units by their names

fit.CopyNumberChromosomalModel

AromaCellCpgFile

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

The Explorer class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getName.AromaTransform

Gets the name of the output data set

fit.CopyNumberSegmentationModel

display.Explorer

Displays the explorer in the default browser

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

segmentByMPCBS.RawGenomicSignals

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

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

setArrays.Explorer

Sets the arrays

getNames.ChromosomalModel

Gets the names of the arrays

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

ChromosomeExplorer

The ChromosomeExplorer class

writeFooter.AromaTabularBinaryFile

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

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

AromaGenomeTextFile

The AromaGenomeTextFile class

getAlias.Explorer

Gets the alias of the output set

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaCellPositionFile

A binary file holding chromosome/position for each cell

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

ChromosomalModel

The ChromosomalModel class

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

The HaarSegModel class

findAnnotationData

Locates an annotation data file

getChromosomes.ChromosomalModel

Gets the chromosomes available

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

nbrOfArrays.ChromosomalModel

Gets the number of arrays

getTags.Explorer

Gets the tags of the explorer

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

process.AromaTransform

Processes the data set

The BinnedScatter class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

The AromaPlatform class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

The CbsModel class

Gets the running time of the R process and its children processes

getChipType.ChromosomalModel

Gets a label for all chip types merged

doCBS.character

Performs CBS segmentation on a data set

setAlias.Explorer

Sets the alias of the output set

setArrays.ChromosomeExplorer

Sets the arrays

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

getPath.AromaTransform

Gets the path of the output data set

The RawCopyNumbers class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

readFooter.AromaTabularBinaryFile

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

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

getOutputDataSet.AromaTransform

Gets the transformed data set

getModel.ChromosomeExplorer

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

RawAlleleBFractions

The RawAlleleBFractions class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getName.Explorer

Gets the name of the explorer

aroma.core-package

Package aroma.core

RawGenomicSignals

The RawGenomicSignals class

Applies patches for a specific package

getTags.AromaTransform

Gets the tags of the output data set

SegmentedCopyNumbers

The SegmentedCopyNumbers class

The UnitNamesFile interface class

getInputDataSet.AromaTransform

Gets the input data set

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaUnitTypesFile

The AromaUnitTypesFile class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

nbrOfArrays.Explorer

Gets the total number of arrays

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

estimateSds.CopyNumberChromosomalModel

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

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

findAnnotationDataByChipType

Locates an annotation data file by its chip type

isDone.AromaTransform

Checks if the data set is processed or not