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aroma.core (version 1.2.0)

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

632

Version

1.2.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

September 10th, 2009

Functions in aroma.core (1.2.0)

extract.AromaMicroarrayDataSetTuple

Extracts a subset AromaMicroarrayDataSetTuple

The Interface class

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

getTags.Explorer

Gets the tags of the explorer

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

The AromaTransform class

getInputDataSet.AromaTransform

Gets the input data set

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

The UnitTypesFile interface class

getPath.AromaTransform

Gets the path of the output data set

display.Explorer

Displays the explorer in the default browser

The Explorer class

AromaUnitTypesFile

The AromaUnitTypesFile class

aroma.core-package

Package aroma.core

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

getAlias.Explorer

Gets the alias of the output set

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

AromaTabularBinarySet

The AromaTabularBinarySet class

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

findAnnotationDataByChipType

Locates an annotation data file by its chip type

The UnitNamesFile interface class

getOutputDataSet.AromaTransform

Gets the transformed data set

process.AromaTransform

Processes the data set

getTags.AromaTransform

Gets the tags of the output data set

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

readFooter.AromaTabularBinaryFile

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

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

getFullName.AromaTransform

Gets the full name of the output data set

UnitAnnotationDataFile

The UnitAnnotationDataFile interface class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

The BinnedScatter class

findAnnotationData

Locates an annotation data file

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

getArrays.Explorer

Gets the names of the arrays

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

Non-documented objects

Non-documented objects

indexOf.UnitNamesFile

Gets the indices of units by their names

The RawCopyNumbers class

setArrays.Explorer

Sets the arrays

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

getName.Explorer

Gets the name of the explorer

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

getTableOfArrays.AromaMicroarrayDataSetTuple

Gets a table of arrays

AromaUnitCallSet

The AromaUnitCallSet class

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

getName.AromaTransform

Gets the name of the output data set

RawSequenceReads

The RawSequenceReads class

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

RawGenomicSignals

The RawGenomicSignals class

writeFooter.AromaTabularBinaryFile

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

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

nbrOfArrays.AromaMicroarrayDataSetTuple

Gets the number of arrays

Applies patches for a specific package

SegmentedCopyNumbers

The SegmentedCopyNumbers class

downloadPackagePatch

Download a package patch

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaUnitCallFile

The AromaUnitCallFile class

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

indexOfArrays.AromaMicroarrayDataSetTuple

Gets the indices of the arrays

setAlias.Explorer

Sets the alias of the output set

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

getArrays.AromaMicroarrayDataSetTuple

Gets the names of the arrays

getArrayTuple.AromaMicroarrayDataSetTuple

Gets arrays across chip types for one sample

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

nbrOfArrays.Explorer

Gets the total number of arrays

AromaTabularBinaryFile

The AromaTabularBinaryFile class

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

isDone.AromaTransform

Checks if the data set is processed or not

RawAlleleBFractions

The RawAlleleBFractions class

The AromaPlatform class

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys