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aroma.core (version 1.3.1)

Support package for aroma.affymetrix et al.

Description

This package is a private support package for aroma.affymetrix et al. The methods and classes of this package are independent of platform. Its API is in alpha and beta stage.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

731

Version

1.3.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

November 3rd, 2009

Functions in aroma.core (1.3.1)

The AromaPlatform class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

The UnitTypesFile interface class

AromaUnitCallSet

The AromaUnitCallSet class

AromaUnitCallFile

The AromaUnitCallFile class

getTableOfArrays.AromaMicroarrayDataSetTuple

Gets a table of arrays

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

getAlias.Explorer

Gets the alias of the output set

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

The UnitNamesFile interface class

Non-documented objects

Non-documented objects

RawGenomicSignals

The RawGenomicSignals class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

RawSequenceReads

The RawSequenceReads class

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

findAnnotationData

Locates an annotation data file

getArrayTuple.AromaMicroarrayDataSetTuple

Gets arrays across chip types for one sample

getName.Explorer

Gets the name of the explorer

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

The AromaTransform class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

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

nbrOfArrays.AromaMicroarrayDataSetTuple

Gets the number of arrays

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

getName.AromaTransform

Gets the name of the output data set

getPath.AromaTransform

Gets the path of the output data set

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

getArrays.Explorer

Gets the names of the arrays

SegmentedCopyNumbers

The SegmentedCopyNumbers class

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getTags.AromaTransform

Gets the tags of the output data set

AromaTabularBinarySet

The AromaTabularBinarySet class

display.Explorer

Displays the explorer in the default browser

downloadPackagePatch

Download a package patch

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

getArrays.AromaMicroarrayDataSetTuple

Gets the names of the arrays

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

AromaTabularBinaryFile

The AromaTabularBinaryFile class

aroma.core-package

Package aroma.core

The RawCopyNumbers class

RawAlleleBFractions

The RawAlleleBFractions class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

writeFooter.AromaTabularBinaryFile

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

process.AromaTransform

Processes the data set

isDone.AromaTransform

Checks if the data set is processed or not

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

getInputDataSet.AromaTransform

Gets the input data set

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

The BinnedScatter class

setAlias.Explorer

Sets the alias of the output set

readFooter.AromaTabularBinaryFile

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

getFullName.AromaTransform

Gets the full name of the output data set

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

AromaUnitTypesFile

The AromaUnitTypesFile class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

The Explorer class

extract.AromaMicroarrayDataSetTuple

Extracts a subset AromaMicroarrayDataSetTuple

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

getOutputDataSet.AromaTransform

Gets the transformed data set

getTags.Explorer

Gets the tags of the explorer

indexOfArrays.AromaMicroarrayDataSetTuple

Gets the indices of the arrays

indexOf.UnitNamesFile

Gets the indices of units by their names

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

findAnnotationDataByChipType

Locates an annotation data file by its chip type

nbrOfArrays.Explorer

Gets the total number of arrays

Applies patches for a specific package

setArrays.Explorer

Sets the arrays