Learn R Programming

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

aroma.core (version 1.8.1)

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.

Copy Link

Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

1.8.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

December 6th, 2010

Functions in aroma.core (1.8.1)

RawSequenceReads

The RawSequenceReads class

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

downloadPackagePatch

Download a package patch

AromaGenomeTextFile

The AromaGenomeTextFile class

The BinnedScatter class

Non-documented objects

Non-documented objects

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

fit.CopyNumberChromosomalModel

The Explorer class

The CbsModel class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

getOutputDataSet.AromaTransform

Gets the transformed data set

RawAlleleBFractions

The RawAlleleBFractions class

AromaUnitCallFile

The AromaUnitCallFile class

readFooter.AromaTabularBinaryFile

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

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

The UnitNamesFile interface class

display.Explorer

Displays the explorer in the default browser

AromaUnitCallSet

The AromaUnitCallSet class

indexOf.UnitNamesFile

Gets the indices of units by their names

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

Applies patches for a specific package

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

getTags.AromaTransform

Gets the tags of the output data set

getNames.ChromosomalModel

Gets the names of the arrays

setArrays.ChromosomeExplorer

Sets the arrays

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

The RawCopyNumbers class

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

writeFooter.AromaTabularBinaryFile

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

The HaarSegModel class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

RawGenomicSignals

The RawGenomicSignals class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

RawCopyNumberModel

The RawCopyNumberModel class

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

process.AromaTransform

Processes the data set

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

aroma.core-package

Package aroma.core

findAnnotationData

Locates an annotation data file

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getNames.Explorer

Gets the names of the input samples

ChromosomeExplorer

The ChromosomeExplorer class

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

The AromaPlatform class

getInputDataSet.AromaTransform

Gets the input data set

ChromosomalModel

The ChromosomalModel class

estimateSds.CopyNumberChromosomalModel

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

getAlias.Explorer

Gets the alias of the output set

nbrOfArrays.Explorer

Gets the total number of arrays

getChromosomes.ChromosomalModel

Gets the chromosomes available

getPath.AromaTransform

Gets the path of the output data set

AromaTabularBinarySet

The AromaTabularBinarySet class

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

isDone.AromaTransform

Checks if the data set is processed or not

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

nbrOfArrays.ChromosomalModel

Gets the number of arrays

segmentByMPCBS.RawGenomicSignals

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

getName.AromaTransform

Gets the name of the output data set

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

setArrays.Explorer

Sets the arrays

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

AromaCellPositionFile

A binary file holding chromosome/position for each cell

The AromaTransform class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getFullName.AromaTransform

Gets the full name of the output data set

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

doCBS.character

Performs CBS segmentation on a data set

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

getChipType.ChromosomalModel

Gets a label for all chip types merged

fit.CopyNumberSegmentationModel

AromaCellCpgFile

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

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

getTags.Explorer

Gets the tags of the explorer

getName.Explorer

Gets the name of the explorer

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

AromaUnitTypesFile

The AromaUnitTypesFile class

The GladModel class

SegmentedCopyNumbers

The SegmentedCopyNumbers class

setAlias.Explorer

Sets the alias of the output set

The UnitTypesFile interface class

getModel.ChromosomeExplorer