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aroma.core (version 1.1.2)

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. It's API is in alpha and beta stage.

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Version

Install

install.packages('aroma.core')

Monthly Downloads

632

Version

1.1.2

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

June 16th, 2009

Functions in aroma.core (1.1.2)

The RawCopyNumbers class

SegmentedGenomicSignalsInterface

The SegmentedGenomicSignalsInterface class interface

colBinnedSmoothing.matrix

Binned smoothing of a matrix column by column

AromaUnitFracBCnBinaryFile

The AromaUnitFracBCnBinaryFile class

aroma.core-package

Package aroma.core

getOutputDataSet.AromaTransform

Gets the transformed data set

fitGenotypeCone.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitTotalCnBinaryFile

The AromaUnitTotalCnBinaryFile class

getPath.AromaTransform

Gets the path of the output data set

The Interface class

AromaMicroarrayTabularBinaryFile

The AromaMicroarrayTabularBinaryFile class

AromaMicroarrayDataFile

The abstract AromaMicroarrayDataFile class

The UnitNamesFile class

getArrays.AromaMicroarrayDataSetTuple

Gets the names of the arrays

getTags.Explorer

Gets the tags of the explorer

getName.Explorer

Gets the name of the explorer

The Explorer class

AromaUnitFracBCnBinarySet

The AromaUnitFracBCnBinarySet class

getTags.AromaTransform

Gets the tags of the output data set

AromaUnitSignalBinarySet

The AromaUnitSignalBinarySet class

allocate.AromaTabularBinaryFile

Creates an AromaTabularBinaryFile

AromaTabularBinaryFile

The AromaTabularBinaryFile class

getFullName.AromaTransform

Gets the full name of the output data set

findAnnotationData

Locates an annotation data file

AromaTabularBinarySet

The AromaTabularBinarySet class

extract.AromaMicroarrayDataSetTuple

Extracts a subset AromaMicroarrayDataSetTuple

AromaUnitSignalBinaryFile

The AromaUnitSignalBinaryFile class

findAnnotationDataByChipType

Locates an annotation data file by its chip type

Applies patches for a specific package

process.AromaTransform

Processes the data set

fitMultiDimensionalCone.matrix

Fits an affine transformation to multi-dimensional data

AromaMicroarrayDataSet

The AromaMicroarrayDataSet class

getTableOfArrays.AromaMicroarrayDataSetTuple

Gets a table of arrays

as.GrayscaleImage.matrix

Creates a Grayscale (TrueColor) Image from a matrix file

estimateStandardDeviation.RawGenomicSignals

Estimates the standard deviation of the raw Ys

AromaUnitTotalCnBinarySet

The AromaUnitTotalCnBinarySet class

matrixBlockPolish.matrix

Applies a polishing function to blocks of rows and columns repeatedly

AromaUnitCallFile

The AromaUnitCallFile class

AromaUnitGenotypeCallFile

The AromaUnitGenotypeCallFile class

RawAlleleBFractions

The RawAlleleBFractions class

indexOfArrays.AromaMicroarrayDataSetTuple

Gets the indices of the arrays

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

SegmentedAlleleBFractions

The SegmentedAlleleBFractions class

AromaCellTabularBinaryFile

The AromaCellTabularBinaryFile class

getName.AromaTransform

Gets the name of the output data set

getInputDataSet.AromaTransform

Gets the input data set

nbrOfArrays.AromaMicroarrayDataSetTuple

Gets the number of arrays

The AromaPlatform class

getArrayTuple.AromaMicroarrayDataSetTuple

Gets arrays across chip types for one sample

getArrays.Explorer

Gets the names of the arrays

indexOf.UnitNamesFile

Gets the indices of units by their names

isDone.AromaTransform

Checks if the data set is processed or not

segmentByHaarSeg.RawGenomicSignals

Segment copy numbers using the HaarSeg method

Non-documented objects

Non-documented objects

process.Explorer

Generates image files, scripts and dynamic pages for the explorer

AromaUnitTabularBinaryFile

The AromaUnitTabularBinaryFile class

writeFooter.AromaTabularBinaryFile

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

AromaUnitGenotypeCallSet

The AromaUnitGenotypeCallSet class

colKernelSmoothing.matrix

Kernel smoothing of a matrix column by column

downloadPackagePatch

Download a package patch

AromaMicroarrayDataSetTuple

The AromaMicroarrayDataSetTuple class

display.Explorer

Displays the explorer in the default browser

SegmentedCopyNumbers

The SegmentedCopyNumbers class

RawMirroredAlleleBFractions

The RawMirroredAlleleBFractions class

segmentByCBS.RawGenomicSignals

Segment copy numbers using the CBS method

mergeBoxplotStats.list

Merges a list of boxplot.stats() elements

RawGenomicSignals

The RawGenomicSignals class

segmentByGLAD.RawGenomicSignals

Segment copy numbers using the GLAD method

The AromaTransform class

getAlias.Explorer

Gets the alias of the output set

setAlias.Explorer

Sets the alias of the output set

nbrOfChipTypes.AromaMicroarrayDataSetTuple

Gets the number of chip types

setArrays.Explorer

Sets the arrays

nbrOfArrays.Explorer

Gets the total number of arrays

readFooter.AromaTabularBinaryFile

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

The BinnedScatter class

fitGenotypeConeBySfit.matrix

Fits an affine transformation to allele A and allele B data

AromaUnitCallSet

The AromaUnitCallSet class