Learn R Programming

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

aroma.core (version 1.9.0)

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.

Copy Link

Version

Install

install.packages('aroma.core')

Monthly Downloads

588

Version

1.9.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

January 10th, 2011

Functions in aroma.core (1.9.0)

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

AromaGenomeTextFile

The AromaGenomeTextFile class

AromaCellCpgFile

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

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

getModel.ChromosomeExplorer

The UnitNamesFile interface class

doCBS.character

Performs CBS segmentation on a data set

isDone.AromaTransform

Checks if the data set is processed or not

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

ChromosomeExplorer

The ChromosomeExplorer class

indexOf.UnitNamesFile

Gets the indices of units by their names

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

Non-documented objects

Non-documented objects

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

writeDataFrame.AromaUnitSignalBinarySet

Writes the data set as a tab-delimited text file

nbrOfArrays.ChromosomalModel

Gets the number of arrays

Applies patches for a specific package

setArrays.ChromosomeExplorer

Sets the arrays

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

writeDataFrame.AromaUnitSignalBinaryFile

Writes the data file as a tab-delimited text file

readFooter.AromaTabularBinaryFile

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

The BinnedScatter class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

getTags.AromaTransform

Gets the tags of the output data set

getTags.Explorer

Gets the tags of the explorer

display.Explorer

Displays the explorer in the default browser

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

The CbsModel class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

getAlias.Explorer

Gets the alias of the output set

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getOutputDataSet.AromaTransform

Gets the transformed data set

RawSequenceReads

The RawSequenceReads class

The AromaPlatform class

getInputDataSet.AromaTransform

Gets the input data set

downloadPackagePatch

Download a package patch

AromaTabularBinarySet

The AromaTabularBinarySet class

AromaTabularBinaryFile

The AromaTabularBinaryFile class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getChromosomes.ChromosomalModel

Gets the chromosomes available

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

process.AromaTransform

Processes the data set

updateSamplesFile.ChromosomeExplorer

Updates the samples.js file

writeDataFrame.AromaUnitTabularBinaryFile

Writes the data file as a tab-delimited text file

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getPath.AromaTransform

Gets the path of the output data set

RawCopyNumberModel

The RawCopyNumberModel class

nbrOfArrays.Explorer

Gets the total number of arrays

setArrays.Explorer

Sets the arrays

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

The HaarSegModel class

AromaUnitTypesFile

The AromaUnitTypesFile class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

getNames.ChromosomalModel

Gets the names of the arrays

The UnitTypesFile interface class

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

The RawCopyNumbers class

RawAlleleBFractions

The RawAlleleBFractions class

RawGenomicSignals

The RawGenomicSignals class

AromaUnitCallFile

The AromaUnitCallFile class

estimateSds.CopyNumberChromosomalModel

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

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

SegmentedCopyNumbers

The SegmentedCopyNumbers class

getName.Explorer

Gets the name of the explorer

writeFooter.AromaTabularBinaryFile

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

The Explorer class

nbrOfChipTypes.ChromosomalModel

Gets the number of chip types

fit.CopyNumberChromosomalModel

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

process.ChromosomeExplorer

Generates image files, scripts and dynamic pages for the explorer

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

getChipType.ChromosomalModel

Gets a label for all chip types merged

getFullName.AromaTransform

Gets the full name of the output data set

aroma.core-package

Package aroma.core

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

CopyNumberSegmentationModel

The CopyNumberSegmentationModel class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

fit.CopyNumberSegmentationModel

getChromosomes.ChromosomeExplorer

Gets the chromosomes available

CopyNumberChromosomalModel

The CopyNumberChromosomalModel class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

getNames.Explorer

Gets the names of the input samples

AromaCellPositionFile

A binary file holding chromosome/position for each cell

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

setAlias.Explorer

Sets the alias of the output set

ChromosomalModel

The ChromosomalModel class

The AromaTransform class

findAnnotationData

Locates an annotation data file

The GladModel class

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

extractRawCopyNumbers.CopyNumberChromosomalModel

Extracts relative copy numbers

getName.AromaTransform

Gets the name of the output data set

segmentByMPCBS.RawGenomicSignals

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