Help for package aroma.core

Version:

3.3.1

Depends:

R (≥ 3.2.1), R.utils (≥ 2.10.1), R.filesets (≥ 2.14.0), R.devices (≥ 2.16.1)

DependsNote:

BioC (>= 3.2)

Imports:

stats, tools, utils, R.methodsS3 (≥ 1.8.1), R.oo (≥ 1.24.0), R.cache (≥ 0.14.0), R.rsp (≥ 0.44.0), matrixStats (≥ 0.57.0), RColorBrewer (≥ 1.1-2), PSCBS (≥ 0.65.0), listenv, future, BiocManager

Suggests:

KernSmooth, png (≥ 0.1-7), Cairo (≥ 1.5-9), EBImage (≥ 4.8.3), preprocessCore (≥ 1.28.0), aroma.light (≥ 2.2.1), DNAcopy (≥ 1.40.0), GLAD (≥ 2.30.0), sfit (≥ 0.1.8), expectile (≥ 0.2.5), HaarSeg (≥ 0.0.2), mpcbs (≥ 1.1.1)

SuggestsNote:

BioC (>= 3.0), Recommended: aroma.light, DNAcopy, png, preprocessCore, sfit

Additional_repositories:

https://henrikbengtsson.r-universe.dev, https://r-forge.r-project.org

Title:

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Description:

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

License:

LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]

URL:

https://github.com/HenrikBengtsson/aroma.core, https://www.aroma-project.org/

BugReports:

https://github.com/HenrikBengtsson/aroma.core/issues

LazyLoad:

TRUE

biocViews:

Microarray, OneChannel, TwoChannel, MultiChannel, DataImport, DataRepresentation, GUI, Visualization, Preprocessing, QualityControl, aCGH, CopyNumberVariants

NeedsCompilation:

Packaged:

2024-02-19 02:33:17 UTC; henrik

Author:

Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]

Maintainer:

Henrik Bengtsson <henrikb@braju.com>

Repository:

CRAN

Date/Publication:

2024-02-19 08:40:02 UTC

Package aroma.core

Description

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

This package is a support package for aroma.affymetrix. This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time. For practical purposes, consider this package a private package.

Installation and updates

This package is available on CRAN, i.e. to install do install.packages("aroma.core").

License

The releases of this package is licensed under LGPL version 2.1 or newer.

The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/

The AbstractCNData class

Description

Package: aroma.core
Class AbstractCNData

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractCNData

Directly known subclasses:
AbstractPSCNData, NonPairedPSCNData, PairedPSCNData

public class AbstractCNData
extends RawGenomicSignals

An AbstractCNData object holds copy number data.

Usage

AbstractCNData(chromosome=NULL, x=NULL, y=NULL, ..., name=NULL, .virtuals=NULL)

Arguments

chromosome

(Optional) An integer scalar (or a vector of length J), which can be used to specify which chromosome each locus belongs to in case multiple chromosomes are segments. This argument is also used for annotation purposes.

x

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

y

Optional numeric vector of J genomic locations.

...

Optional named locus-specific signal vectors of length J.

name

Optional character string.

.virtuals

(Internal) a list with virtual column name functions.

Fields and Methods

Methods:

	`findLargeGaps`	-
	`getChipType`	-
	`getLocusData`	-
	`getPlatform`	-
	`setChipType`	-
	`setPlatform`	-

Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange

Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The AbstractPSCNData class

Description

Package: aroma.core
Class AbstractPSCNData

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AbstractPSCNData

Directly known subclasses:
NonPairedPSCNData, PairedPSCNData

public class AbstractPSCNData
extends AbstractCNData

A AbstractPSCNData object holds parent-specific copy number data.

Usage

AbstractPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, ...)

Arguments

chromosome

x

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

isSNP

An optional logical vector of length J specifying whether each locus is a SNP or not (non-polymorphic loci).

mu

An optional numeric vector of J genotype calls in {0,1/2,1} for AA, AB, and BB, respectively, and NA for non-polymorphic loci.

...

Optional named locus-specific signal vectors of length J.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform

Author(s)

Henrik Bengtsson

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

Description

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

Usage

AromaCellCpgFile(...)

Arguments

...

Arguments passed to constructor of AromaCellTabularBinaryFile.

Details

Note that this class does not assume a rectangular chip layout. In other words, there is no concept of mapping a spatial location on the array to a cell index and vice versa. The reason for this to be able to use this class also for non-rectangular chip types.

Author(s)

Mark Robinson

A binary file holding chromosome/position for each cell

Description

A binary file holding chromosome/position for each cell.

Usage

AromaCellPositionFile(...)

Arguments

...

Arguments passed to constructor of AromaCellTabularBinaryFile.

Details

Author(s)

Henrik Bengtsson

The AromaCellTabularBinaryFile class

Description

Package: aroma.core
Class AromaCellTabularBinaryFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaCellTabularBinaryFile

Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile

public abstract static class AromaCellTabularBinaryFile
extends AromaMicroarrayTabularBinaryFile

An AromaCellTabularBinaryFile is an AromaTabularBinaryFile with the constraint that the rows map one-to-one to the cells (features) of a microarray.

Usage

AromaCellTabularBinaryFile(...)

Arguments

...

Arguments passed to AromaTabularBinaryFile.

Fields and Methods

Methods:

	`byChipType`	-
	`nbrOfCells`	-

Methods inherited from AromaMicroarrayTabularBinaryFile:
allocate, as.character, byChipType, findByChipType, getChipType, getFilenameExtension, getPlatform

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

Author(s)

Henrik Bengtsson

The AromaGenomeTextFile class

Description

Package: aroma.core
Class AromaGenomeTextFile

Directly known subclasses:
AromaUcscGenomeTextFile

public abstract static class AromaGenomeTextFile
extends FileCacheKeyInterface

An AromaGenomeTextFile represents a annotation tabular text file that specifies the number of bases (nucleotides) per chromosome for a particular genome/organism.

Usage

AromaGenomeTextFile(...)

Arguments

...

Arguments passed to TabularTextFile.

Details

An AromaGenomeTextFile is a tab-delimited text file with a header containing (at least) column names 'chromosome' and 'nbrOfBases'. The 'chromosome' column specifies the chromosomes (character strings) and the 'nbrOfBases' column specifies the lengths (integer) of the chromosomes in number of bases (nucleotides).

The filename of an AromaGenomeTextFile should have format "<genome>,chromosomes(,<tag>)*.txt", and be located in annotationData/genomes/<genome>/, e.g. annotationData/genomes/Human/Human,chromosomes,max,20090503.txt.

Fields and Methods

Methods:

	`byGenome`	-
	`readDataFrame`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from TabularTextFile:
as.character, getCommentChar, getDefaultColumnClassPatterns, getDefaultColumnClasses, getDefaultColumnNames, getHeader, getReadArguments, hasColumnHeader, nbrOfLines, nbrOfRows, readColumnNames, readColumns, readDataFrame, readLines, readRawHeader, setCommentChar

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

Examples

# Locate a Human,chromosomes(,.*)*.txt file
db <- AromaGenomeTextFile$byGenome("Human")
print(db)

# Read the data
df <- readDataFrame(db)
print(df)
str(df)

# Details on the file format
oopts <- options(width=40)
print(readLines(db))
options(oopts)

The abstract AromaMicroarrayDataFile class

Description

Package: aroma.core
Class AromaMicroarrayDataFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile

Directly known subclasses:

public abstract static class AromaMicroarrayDataFile
extends FileCacheKeyInterface

An AromaMicroarrayDataFile object represents a single microarray data file. Each such file originates from a specific chip type on a given platform.

Usage

AromaMicroarrayDataFile(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods:

	`getChipType`	-
	`getPlatform`	-
	`isAverageFile`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The AromaMicroarrayDataSet class

Description

Package: aroma.core
Class AromaMicroarrayDataSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSet

Directly known subclasses:

public abstract static class AromaMicroarrayDataSet
extends GenericDataFileSet

An AromaMicroarrayDataSet object represents a set of AromaMicroarrayDataFiles with identical chip types.

Usage

AromaMicroarrayDataSet(files=NULL, ...)

Arguments

files

A list of AromaMicroarrayDataFile:s.

...

Arguments passed to GenericDataFileSet.

Fields and Methods

Methods:

	`as.AromaMicroarrayDataSetList`	-
	`as.AromaMicroarrayDataSetTuple`	-
	`getAverageFile`	-
	`getChipType`	-
	`getPlatform`	-

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName

Author(s)

Henrik Bengtsson

The AromaMicroarrayDataSetTuple class

Description

Package: aroma.core
Class AromaMicroarrayDataSetTuple

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSetList
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSetTuple

Directly known subclasses:
AromaUnitTotalCnBinarySetTuple

public abstract static class AromaMicroarrayDataSetTuple
extends GenericDataFileSetList

Usage

AromaMicroarrayDataSetTuple(..., .setClass="AromaMicroarrayDataSet")

Arguments

...

Arguments passed to GenericDataFileSetList.

.setClass

The name of the class of the input set.

Fields and Methods

Methods:

	`as`	-
	`as.AromaMicroarrayDataSetTuple`	-
	`getChipTypes`	-
	`getFullNames`	-
	`getSets`	-
	`getTags`	-
	`nbrOfChipTypes`	Gets the number of chip types.

Methods inherited from GenericDataFileSetList:
as, as.GenericDataFileSetList, as.character, as.data.frame, as.list, assertDuplicates, clone, extract, getAsteriskTags, getDefaultFullName, getFileList, getFileListClass, getFullNames, getNames, getSet, getSets, getTags, indexOf, length, nbrOfFiles, nbrOfSets, setTags

Author(s)

Henrik Bengtsson

The AromaMicroarrayTabularBinaryFile class

Description

Package: aroma.core
Class AromaMicroarrayTabularBinaryFile

Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile, AromaUnitTabularBinaryFile

public abstract static class AromaMicroarrayTabularBinaryFile
extends AromaPlatformInterface

An AromaMicroarrayTabularBinaryFile is an abstract AromaTabularBinaryFile.

Usage

AromaMicroarrayTabularBinaryFile(...)

Arguments

...

Arguments passed to AromaTabularBinaryFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getFilenameExtension`	-
	`getPlatform`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaPlatform class

Description

Package: aroma.core
Class AromaPlatform

Object
~~|
~~+--AromaPlatform

Directly known subclasses:

public abstract static class AromaPlatform
extends Object

An AromaPlatform provides methods for a given platform, e.g. Affymetrix, Agilent, Illumina.

Usage

AromaPlatform(...)

Arguments

...

Not used.

Methods

Methods:

	`byName`	-
	`equals`	-
	`getAromaUgpFile`	-
	`getName`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-

Author(s)

Henrik Bengtsson

Examples

## Not run: 
 library("aroma.affymetrix")
platform <- AromaPlatform$byName("Affymetrix")
print(platform)
stopifnot(getName(platform) == "Affymetrix")


## End(Not run)

The AromaPlatformInterface class

Description

Package: aroma.core
Class AromaPlatformInterface

Interface
~~|
~~+--AromaPlatformInterface

Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaMicroarrayTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile

public abstract class AromaPlatformInterface
extends Interface

An AromaPlatformInterface provides methods for a given platform, e.g. Affymetrix, Agilent, Illumina.

Usage

AromaPlatformInterface(...)

Arguments

...

Not used.

Methods

Methods:

	`getAromaPlatform`	Gets the platform.
	`getAromaUflFile`	-
	`getAromaUgpFile`	-
	`getChipType`	Gets the chip type.
	`getPlatform`	Gets the platform.
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The AromaRepository class

Description

Package: aroma.core
Class AromaRepository

Object
~~|
~~+--AromaRepository

Directly known subclasses:

public static class AromaRepository
extends Object

An AromaRepository object provides methods for downloading annotation data from the Aroma repository.

Usage

AromaRepository(urlPath="https://www.aroma-project.org/data", verbose=FALSE, ...)

Arguments

urlPath

The URL to the Aroma repository.

verbose

The Verbose to be used during processing.

...

Not used.

Methods

Methods:

	`downloadACC`	-
	`downloadACM`	-
	`downloadACP`	-
	`downloadACS`	-
	`downloadAll`	-
	`downloadCDF`	-
	`downloadChipTypeFile`	Download a particular chip type annotation file.
	`downloadProbeSeqsTXT`	-
	`downloadTXT`	-
	`downloadUFL`	-
	`downloadUGC`	-
	`downloadUGP`	-

Author(s)

Henrik Bengtsson

The AromaTabularBinaryFile class

Description

Package: aroma.core
Class AromaTabularBinaryFile

public abstract static class AromaTabularBinaryFile
extends FileCacheKeyInterface

A AromaTabularBinaryFile represents a file with a binary format. It has a well defined header, a data section, and a footer.

Usage

AromaTabularBinaryFile(...)

Arguments

...

Arguments passed to GenericTabularFile.

Fields and Methods

Methods:

	`[`	-
	`[<-`	-
	`colMeans`	-
	`colSums`	-
	`getBytesPerColumn`	-
	`getColClasses`	-
	`importFrom`	-
	`nbrOfColumns`	-
	`nbrOfRows`	-
	`readColumns`	-
	`readFooter`	Reads the file footer in XML format into a named nested list.
	`subset`	-
	`summary`	-
	`writeFooter`	Writes a named nested list to the file footer in XML format.

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

Creates an AromaTabularBinaryFile

Description

Creates an AromaTabularBinaryFile of a certain dimension and data column types.

Usage

## Static method (use this):
## AromaTabularBinaryFile$allocate(filename, path=NULL, nbrOfRows, types, sizes,
##   signeds=TRUE, defaults=NA, comment=NULL, overwrite=FALSE, skip=FALSE, footer=list(),
##   ..., verbose=FALSE)

## Don't use the below:
## S3 method for class 'AromaTabularBinaryFile'
allocate(static, filename, path=NULL, nbrOfRows, types, sizes, signeds=TRUE, defaults=NA,
  comment=NULL, overwrite=FALSE, skip=FALSE, footer=list(), ..., verbose=FALSE)

Arguments

filename

The filename of the new file.

path

The path where to store the new file.

nbrOfRows

An integer specifying the number of rows to allocate.

types

A character vector specifying the data type of each column. The length specifies the number of columns to allocate.

sizes

An integer vector of values in {1,2,4,8} specifying the size of each column (data type).

signeds

An logical vector specifying if the data types in each column is signed or not.

defaults

An optional list (or vector) containing default values for each column.

comment

An optional character string written to the file header.

overwrite

If TRUE, an existing file is overwritten, otherwise not.

skip

If TRUE and overwrite=TRUE, any existing file is returned as is.

footer

An optional list of attributes written (as character strings) to the file footer.

...

Not used.

verbose

Verbose.

Value

Returns a AromaTabularBinaryFile object.

Data types

Valid data types are currently "integer" and "double".

Author(s)

Henrik Bengtsson

The AromaTabularBinarySet class

Description

Package: aroma.core
Class AromaTabularBinarySet

Directly known subclasses:
AromaUnitCallSet, AromaUnitFracBCnBinarySet, AromaUnitGenotypeCallSet, AromaUnitPscnBinarySet, AromaUnitSignalBinarySet, AromaUnitTotalCnBinarySet

public static class AromaTabularBinarySet
extends GenericTabularFileSet

An AromaTabularBinarySet object represents a set of AromaTabularBinaryFiles with identical chip types.

Usage

AromaTabularBinarySet(files=NULL, ...)

Arguments

files

A list of AromaTabularBinaryFile:s.

...

Arguments passed to GenericDataFileSet.

Fields and Methods

Methods:
No methods defined.

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaTransform class

Description

Package: aroma.core
Class AromaTransform

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform

Directly known subclasses:

public abstract static class AromaTransform
extends ParametersInterface

This abstract class represents a transform (algorithm/operator) that transforms data. A transform has an input data set, which is transformed into an output data set.

Usage

AromaTransform(dataSet=NULL, tags="*", ..., .reqSetClass="AromaMicroarrayDataSet")

Arguments

dataSet

The input data set as an AromaMicroarrayDataSet.

tags

A character vector of tags to be appended to the tags of the input data set.

...

Not used.

.reqSetClass

Internal argument.

Details

Subclasses must implement the process() method.

Fields and Methods

Methods:

	`getFullName`	Gets the full name of the output data set.
	`getInputDataSet`	Gets the input data set.
	`getName`	Gets the name of the output data set.
	`getOutputDataSet`	Gets the transformed data set.
	`getPath`	Gets the path of the output directory.
	`getRootPath`	Gets the root path of the output directory.
	`getTags`	Gets the tags of the output data set.
	`isDone`	Checks if the data set is processed or not.
	`process`	Processes the data set.
	`setTags`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AromaUnitCallFile class

Description

Package: aroma.core
Class AromaUnitCallFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallFile

Directly known subclasses:
AromaUnitGenotypeCallFile

public static class AromaUnitCallFile
extends AromaUnitSignalBinaryFile

An AromaUnitCallFile is a AromaUnitSignalBinaryFile.

Usage

AromaUnitCallFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

Methods:

	`extractCallArray`	-
	`extractCalls`	-
	`extractMatrix`	-
	`findUnitsTodo`	-

Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitCallSet class

Description

Package: aroma.core
Class AromaUnitCallSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallSet

Directly known subclasses:
AromaUnitGenotypeCallSet

public static class AromaUnitCallSet
extends AromaUnitSignalBinarySet

An AromaUnitCallSet object represents a set of AromaUnitCallFiles with identical chip types.

Usage

AromaUnitCallSet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`extractCallArray`	-
	`extractCalls`	-
	`extractGenotypeMatrix`	-
	`findUnitsTodo`	-

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaUnitFracBCnBinaryFile class

Description

Package: aroma.core
Class AromaUnitFracBCnBinaryFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitFracBCnBinaryFile

Directly known subclasses:

public static class AromaUnitFracBCnBinaryFile
extends AromaUnitSignalBinaryFile

An AromaUnitFracBCnBinaryFile is a AromaUnitTabularBinaryFile.

Usage

AromaUnitFracBCnBinaryFile(...)

Arguments

...

Arguments passed to AromaUnitTabularBinaryFile.

Fields and Methods

Methods:

	`extractRawAlleleBFractions`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitFracBCnBinarySet class

Description

Package: aroma.core
Class AromaUnitFracBCnBinarySet

Directly known subclasses:

public static class AromaUnitFracBCnBinarySet
extends AromaUnitSignalBinarySet

An AromaUnitFracBCnBinarySet object represents a set of AromaUnitFracBCnBinaryFiles with identical chip types.

Usage

AromaUnitFracBCnBinarySet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Details

The term "allele B fraction" is also know as "allele B frequency", which was coined by Peiffer et al. (2006). Note that the term "frequency" is a bit misleading since it is not a frequency in neither the statistical nor the population sense, but rather only proportion relative to the total amount of allele A and allele B signals, which is calculated for each sample independently.

Fields and Methods

Methods:

	`byName`	-
	`writeDataFrame`	-

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

References

[1] Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping, Genome Res, 2006.

The AromaUnitGenotypeCallFile class

Description

Package: aroma.core
Class AromaUnitGenotypeCallFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitGenotypeCallFile

Directly known subclasses:

public static class AromaUnitGenotypeCallFile
extends AromaUnitCallFile

An AromaUnitGenotypeCallFile is a AromaUnitTabularBinaryFile.

Usage

AromaUnitGenotypeCallFile(...)

Arguments

...

Arguments passed to AromaUnitTabularBinaryFile.

Fields and Methods

Methods:

	`extractGenotypeMatrix`	-
	`extractGenotypes`	-
	`isHeterozygous`	-
	`isHomozygous`	-
	`updateGenotypes`	-

Methods inherited from AromaUnitCallFile:
allocate, extractCallArray, extractCalls, extractMatrix, findUnitsTodo

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitGenotypeCallSet class

Description

Package: aroma.core
Class AromaUnitGenotypeCallSet

Directly known subclasses:

public static class AromaUnitGenotypeCallSet
extends AromaUnitCallSet

An AromaUnitGenotypeCallSet object represents a set of AromaUnitGenotypeCallFiles with identical chip types.

Usage

AromaUnitGenotypeCallSet(...)

Arguments

...

Arguments passed to AromaUnitCallSet.

Fields and Methods

Methods:

	`byName`	-
	`extractGenotypes`	-

Methods inherited from AromaUnitCallSet:
byPath, extractCallArray, extractCalls, extractGenotypeMatrix, findByName, findUnitsTodo

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaUnitPscnBinaryFile class

Description

Package: aroma.core
Class AromaUnitPscnBinaryFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitPscnBinaryFile

Directly known subclasses:

public abstract static class AromaUnitPscnBinaryFile
extends CopyNumberDataFile

An AromaUnitPscnBinaryFile is a AromaUnitSignalBinaryFile that holds total copy number signals (TCNs) and allele B fractions (BAFs). The TCNs can either be on an unknown scale or ratios relative to a reference. The signals are always stored on the original scale, i.e. they are never stored on the logaritmic scale. The BAFs are always on a [0-eps,1+eps] scale, where eps >= 0.

Usage

AromaUnitPscnBinaryFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

Methods:

	`extractRawCopyNumbers`	-
	`hasAlleleBFractions`	-
	`hasStrandiness`	-
	`hasTotalCopyNumberRatios`	-

Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitPscnBinarySet class

Description

Package: aroma.core
Class AromaUnitPscnBinarySet

Directly known subclasses:

public static class AromaUnitPscnBinarySet
extends CopyNumberDataSet

An AromaUnitPscnBinarySet object represents a set of AromaUnitPscnBinaryFiles with identical chip types.

Usage

AromaUnitPscnBinarySet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`byName`	-
	`getAverageFile`	-
	`writeDataFrame`	-

Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaUnitSignalBinaryFile class

Description

Package: aroma.core
Class AromaUnitSignalBinaryFile

Directly known subclasses:
AromaUnitCallFile, AromaUnitFracBCnBinaryFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile

public static class AromaUnitSignalBinaryFile
extends AromaPlatformInterface

An AromaUnitSignalBinaryFile is a AromaTabularBinaryFile.

Usage

AromaUnitSignalBinaryFile(...)

Arguments

...

Arguments passed to AromaTabularBinaryFile.

Fields and Methods

Methods:

	`extractMatrix`	-
	`getChipType`	-
	`getNumberOfFilesAveraged`	-
	`getPlatform`	-
	`isAverageFile`	-
	`nbrOfUnits`	-
	`readDataFrame`	-
	`writeDataFrame`	Writes the data file as a tab-delimited text file.

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitSignalBinarySet class

Description

Package: aroma.core
Class AromaUnitSignalBinarySet

Directly known subclasses:
AromaUnitCallSet, AromaUnitFracBCnBinarySet, AromaUnitGenotypeCallSet, AromaUnitPscnBinarySet, AromaUnitTotalCnBinarySet

public static class AromaUnitSignalBinarySet
extends AromaTabularBinarySet

An AromaUnitSignalBinarySet object represents a set of AromaUnitSignalBinaryFiles with identical chip types.

Usage

AromaUnitSignalBinarySet(...)

Arguments

...

Arguments passed to AromaTabularBinarySet.

Fields and Methods

Methods:

	`byName`	-
	`getAromaUgpFile`	-
	`getChipType`	-
	`getPlatform`	-
	`writeDataFrame`	Writes the data set as a tab-delimited text file.

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaUnitTabularBinaryFile class

Description

Package: aroma.core
Class AromaUnitTabularBinaryFile

Directly known subclasses:
AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile

public abstract static class AromaUnitTabularBinaryFile
extends UnitAnnotationDataFile

A AromaUnitTabularBinaryFile is an AromaTabularBinaryFile with the constraint that the rows map one-to-one to, and in the same order as, the units in a annotation chip type file (e.g. CDF file). The (full) chip type of the annotation chip type file is given by the mandatory file footer chipType.

Usage

AromaUnitTabularBinaryFile(...)

Arguments

...

Arguments passed to AromaTabularBinaryFile.

Fields and Methods

Methods:

	`byChipType`	-
	`nbrOfUnits`	-
	`writeDataFrame`	Writes the data file as a tab-delimited text file.

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from AromaMicroarrayTabularBinaryFile:
allocate, as.character, byChipType, findByChipType, getChipType, getFilenameExtension, getPlatform

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitTotalCnBinaryFile class

Description

Package: aroma.core
Class AromaUnitTotalCnBinaryFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTotalCnBinaryFile

Directly known subclasses:

public abstract static class AromaUnitTotalCnBinaryFile
extends CopyNumberDataFile

An AromaUnitTotalCnBinaryFile is a AromaUnitSignalBinaryFile.

Usage

AromaUnitTotalCnBinaryFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

Methods:

	`extractPSCNArray`	-
	`extractPSCNMatrix`	-
	`extractRawCopyNumbers`	-
	`getAM`	-
	`hasAlleleBFractions`	-
	`hasStrandiness`	-

Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The AromaUnitTotalCnBinarySet class

Description

Package: aroma.core
Class AromaUnitTotalCnBinarySet

Directly known subclasses:

public static class AromaUnitTotalCnBinarySet
extends CopyNumberDataSet

An AromaUnitTotalCnBinarySet object represents a set of AromaUnitTotalCnBinaryFiles with identical chip types.

Usage

AromaUnitTotalCnBinarySet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`as.AromaUnitTotalCnBinarySetTuple`	-
	`as.CopyNumberDataSetTuple`	-
	`byName`	-
	`exportAromaUnitPscnBinarySet`	-
	`exportTotalCnRatioSet`	-
	`extractPSCNArray`	-
	`getAverageFile`	-
	`getUnitNamesFile`	-
	`writeDataFrame`	-

Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The AromaUnitTypesFile class

Description

Package: aroma.core
Class AromaUnitTypesFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTypesFile

Directly known subclasses:

public static class AromaUnitTypesFile
extends UnitTypesFile

Usage

AromaUnitTypesFile(...)

Arguments

...

Arguments passed to AromaUnitTabularBinaryFile.

Fields and Methods

Methods:

	`getChipType`	-
	`getPlatform`	-
	`getUnitTypes`	-
	`importFromUnitTypesFile`	-

Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The BinnedScatter class

Description

Package: aroma.core
Class BinnedScatter

list
~~|
~~+--BinnedScatter

Directly known subclasses:

public class BinnedScatter
extends list

Usage

BinnedScatter(data=NULL, density=NULL, map=NULL, params=NULL)

Arguments

data

A Nx2 numeric matrix.

density

...

map

...

params

A list of parameters.

Fields and Methods

Methods:

	`plot`	-
	`points`	-
	`reorder`	-
	`subsample`	-
	`subset`	-

Methods inherited from list:
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.CopyNumberDataSetTuple, as.data.frame, attachLocally, callHooks, coerce,ANY,list-method, exportAromaUnitPscnBinarySet, listToXml, mergeBoxplotStats, relist, type.convert, within

Author(s)

Henrik Bengtsson

Examples

# Sample scatter data
n <- 10e3
x <- rnorm(n=n)
y <- rnorm(n=n)
xy <- cbind(x=x, y=sin(x)+y/5)

# Bin data and estimate densities
xyd <- binScatter(xy)

layout(matrix(1:4, nrow=2))
par(mar=c(5,4,2,1))

# Plot data
plot(xyd, pch=1)

# Thin scatter data by subsampling
rhos <- c(1/3, 1/4, 1/6)
for (kk in seq_along(rhos)) {
  xyd2 <- subsample(xyd, size=rhos[kk])
  points(xyd2, pch=1, col=kk+1)
}

for (kk in seq_along(rhos)) {
  xyd2 <- subsample(xyd, size=rhos[kk])
  plot(xyd2, pch=1, col=kk+1)
  mtext(side=3, line=0, sprintf("Density: %.1f%%", 100*rhos[kk]))
}

The CacheKeyInterface class interface

Description

Package: aroma.core
Class CacheKeyInterface

Interface
~~|
~~+--CacheKeyInterface

Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaGenomeTextFile, AromaMicroarrayDataFile, AromaMicroarrayTabularBinaryFile, AromaTabularBinaryFile, AromaUcscGenomeTextFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile, CbsSegmentationDataFile, FileCacheKeyInterface, SampleAnnotationFile, SegmentationDataFile, TextUnitNamesFile

public class CacheKeyInterface
extends Interface

Usage

CacheKeyInterface(...)

Arguments

...

Not used.

Fields and Methods

Methods:

	`getCacheKey`	Gets a list of cache key items.

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The CbsModel class

Description

Package: aroma.core
Class CbsModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CopyNumberSegmentationModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--CbsModel

Directly known subclasses:

public static class CbsModel
extends CopyNumberSegmentationModel

This class represents the Circular Binary Segmentation (CBS) model [1].

Usage

CbsModel(cesTuple=NULL, ..., seed=NULL)

Arguments

cesTuple

A CopyNumberDataSetTuple.

...

Arguments passed to the constructor of CopyNumberSegmentationModel.

seed

An (optional) integer that if specified will (temporarily) set the random seed each time before calling the segmentation method. For more information, see segmentByCBS().

Fields and Methods

Methods:
No methods defined.

Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions

Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference

Methods inherited from ChromosomalModel:
as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome

Author(s)

Henrik Bengtsson

References

[1] Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572, 2004.
[2] Venkatraman, E. S. & Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 2007.

The ChromosomalModel class

Description

Package: aroma.core
Class ChromosomalModel

Object
~~|
~~+--ChromosomalModel

Directly known subclasses:
CbsModel, CopyNumberChromosomalModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel

public abstract static class ChromosomalModel
extends Object

This abstract class represents a chromosomal model.

Usage

ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", chromosomes=NULL, ...)

Arguments

cesTuple

A AromaMicroarrayDataSetTuple.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

chromosomes

(optional) A vector specifying which chromosomes to process.

...

Not used.

Fields and Methods

Methods:

	`fit`	-
	`getChipType`	Gets a label for all chip types merged.
	`getChipTypes`	-
	`getChromosomes`	Gets the chromosomes to be processed.
	`getFullName`	-
	`getFullNames`	-
	`getGenome`	-
	`getName`	-
	`getNames`	Gets the names of the arrays.
	`getPath`	-
	`getSets`	-
	`getTags`	-
	`indexOf`	-
	`nbrOfArrays`	Gets the number of arrays.
	`nbrOfChipTypes`	Gets the number of chip types.
	`setChromosomes`	-
	`setGenome`	-

Requirements

This class requires genome information annotation files for every chip type.

Author(s)

Henrik Bengtsson

The ChromosomeExplorer class

Description

Package: aroma.core
Class ChromosomeExplorer

Object
~~|
~~+--Explorer
~~~~~~~|
~~~~~~~+--ChromosomeExplorer

Directly known subclasses:

public static class ChromosomeExplorer
extends Explorer

Usage

ChromosomeExplorer(model=NULL, zooms=2^(0:6), ...)

Arguments

model

A CopyNumberChromosomalModel object.

zooms

An positive integer vector specifying for which zoom levels the graphics should be generated.

...

Not used.

Fields and Methods

Methods:

	`display`	-
	`getChromosomes`	Gets the chromosomes available.
	`getFullNames`	-
	`getModel`	Gets the model.
	`getNames`	-
	`getPath`	-
	`getZooms`	-
	`indexOf`	-
	`process`	Generates image files, scripts and dynamic pages for the explorer.
	`setArrays`	Sets the arrays.
	`setCytoband`	-
	`setZooms`	-

Methods inherited from Explorer:
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile

Generating PNG images

In order to get better looking graphs, but also to be able to generate bitmap images on systems without direct bitmap support, which is the case when running R in batch mode or on Unix without X11 support, images are created using the png2 device (a wrapper for bitmap() imitating png()). The png() is only used if png2(), which requires Ghostscript, does not. Note, when images are created using png2(), the images does not appear immediately, although the function call is completed, so be patient.

Author(s)

Henrik Bengtsson

The CopyNumberChromosomalModel class

Description

Package: aroma.core
Class CopyNumberChromosomalModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel

Directly known subclasses:
CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel

public abstract static class CopyNumberChromosomalModel
extends ChromosomalModel

This abstract class represents a copy-number model.

Usage

CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*",
  genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)

Arguments

cesTuple

A CopyNumberDataSetTuple.

refTuple

An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTuple for pairwise comparisons.

calculateRatios

A logical specifying whether ratios should be calculated relative to the reference. If FALSE, argument refTuple is ignored.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

chromosomes

(optional) A vector specifying which chromosomes to process.

maxNAFraction

A double in [0,1] indicating how many non-finite signals are allowed in the sanity checks of the data.

...

Optional arguments that may be used by some of the subclass models.

Fields and Methods

Methods:

	`extractRawCopyNumbers`	Extracts relative copy numbers.
	`fit`	Fits the model.
	`getChromosomeLength`	-
	`getNames`	-
	`getReference`	-
	`isPaired`	-

Requirements

This class requires genome information annotation files for every chip type.

Author(s)

Henrik Bengtsson

The CopyNumberSegmentationModel class

Description

Package: aroma.core
Class CopyNumberSegmentationModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CopyNumberSegmentationModel

Directly known subclasses:
CbsModel, GladModel, HaarSegModel

public abstract static class CopyNumberSegmentationModel
extends CopyNumberChromosomalModel

This abstract class represents a copy-number segmentation model.

Usage

CopyNumberSegmentationModel(...)

Arguments

...

Arguments passed to constructor CopyNumberChromosomalModel.

Fields and Methods

Methods:

	`fit`	Fits the model.
	`getFullNames`	-
	`getRegions`	-
	`getTags`	-
	`plot`	-
	`writeRegions`	-

Author(s)

Henrik Bengtsson

The Explorer class

Description

Package: aroma.core
Class Explorer

Object
~~|
~~+--Explorer

Directly known subclasses:
ChromosomeExplorer

public abstract static class Explorer
extends Object

Usage

Explorer(tags="*", version="0", ...)

Arguments

tags

A character vector of tags to be added to the output path.

version

An optional character string.

...

Not used.

Fields and Methods

Methods:

	`display`	Displays the explorer in the default browser.
	`getFullName`	-
	`getName`	Gets the name of the explorer.
	`getNames`	Gets the names of the input samples.
	`getPath`	Gets the path of the output directory.
	`getRootPath`	Gets the root path of the output directory.
	`getTags`	Gets the tags of the explorer.
	`getVersion`	-
	`nbrOfArrays`	Gets the total number of arrays.
	`process`	Generates image files, scripts and dynamic pages for the explorer.
	`setArrays`	Sets the arrays.

Output directory structure

The main directory of an Explorer report is reports/<name>/<subname>/. The <name> is typically the same as the name of the input data set, and the <subname> is typically the tags of ditto. This main directory is where main HTML document is stored.

For each chip type, real or "virtual" (combined), there is a subdirectory with the same name as the chip type, i.e. reports/<name>/<subname>/<chiptype>/.

For each chip type directory, there are set of subdirectories each specifying a so called image layer, e.g. an image layer showing the raw data, another containing the estimates of a model fit and so on. Path format: reports/<name>/<subname>/<chiptype>/<image layer>/. In this directory all image files are stored, e.g. PNG files.

In some cases one do not want to all input tags to become part of the subname, but instead for instance use those to name the image layer(s). In such cases one has to override the default names.

Author(s)

Henrik Bengtsson

The FileCacheKeyInterface class interface

Description

Package: aroma.core
Class FileCacheKeyInterface

Interface
~~|
~~+--CacheKeyInterface
~~~~~~~|
~~~~~~~+--FileCacheKeyInterface

Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaGenomeTextFile, AromaMicroarrayDataFile, AromaMicroarrayTabularBinaryFile, AromaTabularBinaryFile, AromaUcscGenomeTextFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile, CbsSegmentationDataFile, SampleAnnotationFile, SegmentationDataFile, TextUnitNamesFile

public class FileCacheKeyInterface
extends CacheKeyInterface

Usage

FileCacheKeyInterface(...)

Arguments

...

Not used.

Fields and Methods

Methods:

	`getCacheKey`	Gets a list of cache key items.

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The GladModel class

Description

Package: aroma.core
Class GladModel

Directly known subclasses:

public static class GladModel
extends CopyNumberSegmentationModel

This class represents the Gain and Loss Analysis of DNA regions (GLAD) model [1]. This class can model chip-effect estimates obtained from multiple chip types, and not all samples have to be available on all chip types.

Usage

GladModel(cesTuple=NULL, ...)

Arguments

cesTuple

A CopyNumberDataSetTuple.

...

Arguments passed to the constructor of CopyNumberSegmentationModel.

Details

Data from multiple chip types are combined "as is". This is based on the assumption that the relative chip effect estimates are non-biased (or at the equally biased across chip types). Note that in GLAD there is no way to down weight certain data points, which is why we can control for differences in variance across chip types.

Fields and Methods

Methods:

	`writeRegions`	-

Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions

Benchmarking

In high-density copy numbers analysis, the most time consuming step is fitting the GLAD model. The complexity of the model grows more than linearly (squared? exponentially?) with the number of data points in the chromosome and sample being fitted. This is why it take much more than twice the time to fit two chip types together than separately.

Author(s)

Henrik Bengtsson

References

[1] Hupe P et al. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics, 2004, 20, 3413-3422.

The HaarSegModel class

Description

Package: aroma.core
Class HaarSegModel

Directly known subclasses:

public static class HaarSegModel
extends CopyNumberSegmentationModel

This class represents the Haar wavelet-based segmentation (HaarSeg) model [1].

Usage

HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)

Arguments

cesTuple

A CopyNumberDataSetTuple.

breaksFdrQ

Default tuning parameters specific to the HaarSeg algorithm.

...

Arguments passed to the constructor of CopyNumberSegmentationModel.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions

Author(s)

Henrik Bengtsson

References

[1] Ben-Yaacov E. and Eldar YC. A fast and flexible method for the segmentation of aCGH data, Bioinformatics, 2008. https://www.weizmann.ac.il/math/yonina/software-hardware/software/haarseg-fast-and-flexible-microarray-segmentation

Non-documented objects

Description

This page contains aliases for all "non-documented" objects that R CMD check detects in this package.

Almost all of them are generic functions that have specific document for the corresponding method coupled to a specific class. Other functions are re-defined by setMethodS3() to default methods. Neither of these two classes are non-documented in reality. The rest are deprecated methods.

Author(s)

Henrik Bengtsson

The NonPairedPSCNData class

Description

Package: aroma.core
Class NonPairedPSCNData

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--NonPairedPSCNData

Directly known subclasses:

public class NonPairedPSCNData
extends AbstractPSCNData

A NonPairedPSCNData object holds parent-specific copy number data. Two NonPairedPSCNData objects for a matched tumor-normal pair can be combined into a PairedPSCNData object.

Usage

NonPairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, C=NULL, beta=NULL, ...)

Arguments

C

A numeric vector of J tumor total copy number (TCN) ratios in [0,+Inf) (due to noise, small negative values are also allowed). The TCN ratios are typically scaled such that copy-neutral diploid loci have a mean of two.

beta

A numeric vector of J tumor allele B fractions (BAFs) in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.

mu

An optional numeric vector of J genotype calls in {0,1/2,1} for AA, AB, and BB, respectively, and NA for non-polymorphic loci. If not given, they are estimated from the normal BAFs using callNaiveGenotypes as described in [2].

isSNP

An optional logical vector of length J specifying whether each locus is a SNP or not (non-polymorphic loci).

chromosome

x

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

...

Optional named locus-specific signal vectors of length J.

Fields and Methods

Methods:

	`as`	-
	`as.NonPairedPSCNData`	-
	`as.PairedPSCNData`	-
	`callNaiveGenotypes`	-
	`callSegmentationOutliers`	-
	`dropSegmentationOutliers`	-
	`getSignalColumnNames`	-
	`segmentByCBS`	-

Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields

Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The PairedPSCNData class

Description

Package: aroma.core
Class PairedPSCNData

Directly known subclasses:

public class PairedPSCNData
extends AbstractPSCNData

A PairedPSCNData object holds paired tumor-normal parent-specific copy number data.

Usage

PairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL,
  CN=NULL, betaN=NULL, ...)

Arguments

CT

CN

An optional numeric vector of J normal TCN ratios.

betaT

A numeric vector of J tumor allele B fractions (BAFs) in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.

betaN

A numeric vector of J matched normal BAFs in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.

muN

isSNP

An optional logical vector of length J specifying whether each locus is a SNP or not (non-polymorphic loci).

chromosome

x

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

...

Optional named locus-specific signal vectors of length J.

Fields and Methods

Methods:

	`as`	-
	`as.PairedPSCNData`	-
	`callNaiveGenotypes`	-
	`callSegmentationOutliers`	-
	`dropSegmentationOutliers`	-
	`getSignalColumnNames`	-
	`getTCNs`	-
	`getTotalCopyNumbers`	-
	`normalizeTumorBoost`	-
	`plotTracks`	-
	`segmentByCBS`	-
	`segmentByPairedPSCBS`	-

Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields

Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The ParametersInterface class interface

Description

Package: aroma.core
Class ParametersInterface

Interface
~~|
~~+--ParametersInterface

Directly known subclasses:
AromaTransform

public class ParametersInterface
extends Interface

Usage

ParametersInterface(...)

Arguments

...

Not used.

Fields and Methods

Methods:

	`getParameters`	-
	`getParametersAsString`	-

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The RawAlleleBFractions class

Description

Package: aroma.core
Class RawAlleleBFractions

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawAlleleBFractions

Directly known subclasses:
RawMirroredAlleleBFractions, SegmentedAlleleBFractions

public class RawAlleleBFractions
extends RawGenomicSignals

Usage

RawAlleleBFractions(...)

Arguments

...

Arguments passed to RawGenomicSignals.

Fields and Methods

Methods:

	`extractRawMirroredAlleleBFractions`	-
	`plot`	-

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The RawCopyNumberModel class

Description

Package: aroma.core
Class RawCopyNumberModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawCopyNumberModel

Directly known subclasses:

public abstract static class RawCopyNumberModel
extends CopyNumberChromosomalModel

This class represents an identity copy-number model which returns the input as is.

Usage

RawCopyNumberModel(...)

Arguments

...

Passed to the constructor of the superclass.

Fields and Methods

Methods:
No methods defined.

Author(s)

Henrik Bengtsson

The RawCopyNumbers class

Description

Package: aroma.core
Class RawCopyNumbers

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawCopyNumbers

Directly known subclasses:
SegmentedCopyNumbers

public class RawCopyNumbers
extends RawGenomicSignals

Usage

RawCopyNumbers(cn=NULL, ...)

Arguments

cn

A numeric vector of length J specifying the copy number at each loci.

...

Arguments passed to RawGenomicSignals.

Fields and Methods

Methods:

	`cnRange`	-
	`extractRawCopyNumbers`	-
	`getSignals`	-
	`plot`	-

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Number of loci
J <- 1000

mu <- double(J)
mu[200:300] <- mu[200:300] + 1
mu[650:800] <- mu[650:800] - 1
eps <- rnorm(J, sd=1/2)
y <- mu + eps
x <- sort(runif(length(y), max=length(y)))


cn <- RawCopyNumbers(y, x)
print(cn)

cn2 <- extractSubset(cn, subset=xSeq(cn, by=5))
print(cn2)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Plot along genome
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, ylim=c(-3,3))
title(main="Complete and subsetted loci")
points(cn2, col="red", pch=176, cex=2)

legend("topright", pch=c(19,176), col=c("#999999", "red"),
       sprintf(c("raw [n=%d]", "every 5th [n=%d]"),
               c(nbrOfLoci(cn), nbrOfLoci(cn2))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Binned smoothing
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Binned smoothing")

cnSa <- binnedSmoothing(cn, by=3)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- binnedSmoothing(cn, by=9)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Binned smoothing (by count)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Binned smoothing (by count)")

cnSa <- binnedSmoothing(cn, by=3, byCount=TRUE)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- binnedSmoothing(cn, by=9, byCount=TRUE)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "BinO(w=3) [n=%d]", "BinO(w=9) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Kernel smoothing (default is Gaussian)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Kernel smoothing w/ Gaussian kernel")

cnSa <- kernelSmoothing(cn, h=2)
points(cnSa, col="blue")

cnSb <- kernelSmoothing(cn, h=5)
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Kernel smoothing
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Kernel smoothing w/ uniform kernel")

xOut <- xSeq(cn, by=10)
cnSa <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=2)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=5)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "U(w=2) [n=%d]", "U(w=5) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")

The RawGenomicSignals class

Description

Package: aroma.core
Class RawGenomicSignals

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals

Directly known subclasses:
AbstractCNData, AbstractPSCNData, NonPairedPSCNData, PairedPSCNData, RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions, RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers

public class RawGenomicSignals
extends RichDataFrame

Usage

RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=0L, name=NULL, ...)

Arguments

y

A numeric vector of length J specifying the signal at each locus.

x

A (optional) numeric vector of length J specifying the position of each locus.

w

A (optional) non-negative numeric vector of length J specifying a weight of each locus.

chromosome

An (optional) integer specifying the chromosome for these genomic signals.

name

An (optional) character string specifying the sample name.

...

Not used.

Fields and Methods

Methods:

	`*`	-
	`+`	-
	`-`	-
	`addBy`	-
	`append`	-
	`as.data.frame`	-
	`binnedSmoothing`	-
	`divideBy`	-
	`drawDensity`	-
	`estimateStandardDeviation`	-
	`gaussianSmoothing`	-
	`getChromosome`	-
	`getChromosomes`	-
	`getPositions`	-
	`getSigma`	-
	`getSignals`	-
	`getWeights`	-
	`getXScale`	-
	`getYScale`	-
	`hasWeights`	-
	`kernelSmoothing`	-
	`lines`	-
	`multiplyBy`	-
	`nbrOfChromosomes`	-
	`nbrOfLoci`	-
	`plot`	-
	`points`	-
	`segmentByCBS`	-
	`segmentByGLAD`	-
	`segmentByHaarSeg`	-
	`segmentByMPCBS`	-
	`setSigma`	-
	`setSignals`	-
	`setWeights`	-
	`setXScale`	-
	`setYScale`	-
	`signalRange`	-
	`sort`	-
	`subtractBy`	-
	`xMax`	-
	`xMin`	-
	`xRange`	-
	`xSeq`	-
	`yMax`	-
	`yMin`	-
	`yRange`	-

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The RawMirroredAlleleBFractions class

Description

Package: aroma.core
Class RawMirroredAlleleBFractions

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawAlleleBFractions
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--RawMirroredAlleleBFractions

Directly known subclasses:

public class RawMirroredAlleleBFractions
extends RawAlleleBFractions

Usage

RawMirroredAlleleBFractions(...)

Arguments

...

Arguments passed to RawAlleleBFractions.

Fields and Methods

Methods:

	`plot`	-

Methods inherited from RawAlleleBFractions:
extractRawMirroredAlleleBFractions, plot

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The RawSequenceReads class

Description

Package: aroma.core
Class RawSequenceReads

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawSequenceReads

Directly known subclasses:

public class RawSequenceReads
extends RawGenomicSignals

Usage

RawSequenceReads(x=NULL, y=rep(1L, length(x)), ...)

Arguments

x

An integer vector of length J specifying the read positions.

y

An (optional) integer vector of length J specifying the number of reads at each position. Default is one read per position.

...

Arguments passed to RawGenomicSignals.

Fields and Methods

Methods:

	`binnedSums`	-
	`extractRawCopyNumbers`	-
	`nbrOfReads`	-
	`plot`	-

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The SegmentedAlleleBFractions class

Description

Package: aroma.core
Class SegmentedAlleleBFractions

Directly known subclasses:

public class SegmentedAlleleBFractions
extends SegmentedGenomicSignalsInterface

Usage

SegmentedAlleleBFractions(..., states=NULL)

Arguments

...

Arguments passed to RawAlleleBFractions.

states

A function returning the copy-number states given a vector of locus positions.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SegmentedGenomicSignalsInterface:
as.data.frame, binnedSmoothingByState, extractSubsetByState, findChangePointsByState, getStateColorMap, getStateColors, getStates, getUniqueStates, getVirtualField, getVirtualLocusFields, kernelSmoothingByState, plot, points, setStateColorMap, setStates

Methods inherited from RawAlleleBFractions:
extractRawMirroredAlleleBFractions, plot

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

The SegmentedCopyNumbers class

Description

Package: aroma.core
Class SegmentedCopyNumbers

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawCopyNumbers
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--SegmentedGenomicSignalsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--SegmentedCopyNumbers

Directly known subclasses:

public class SegmentedCopyNumbers
extends SegmentedGenomicSignalsInterface

Usage

SegmentedCopyNumbers(..., states=NULL)

Arguments

...

Arguments passed to RawCopyNumbers.

states

A function returning the copy-number states given a vector of locus positions.

Fields and Methods

Methods:
No methods defined.

Methods inherited from RawCopyNumbers:
cnRange, extractRawCopyNumbers, getCNs, getCn, getSignals, plot

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# True CN states
stateFcn <- function(x, ...) {
  states <- integer(length(x))
  states[200 <=x & x <= 300] <- -1L
  states[650 <=x & x <= 800] <- +1L
  states
}

# Number of loci
J <- 1000

y <- rnorm(J, sd=1/2)
x <- 1:length(y)
for (state in c(-1,+1)) {
  idxs <- (stateFcn(x) == state)
  y[idxs] <- y[idxs] + state
}


cn <- SegmentedCopyNumbers(y, x, states=stateFcn)
print(cn)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Subsetting
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, ylim=c(-4,4))
title("Copy numbers annotated by state (and subset by state)")

cnS <- extractSubsetByState(cn, states=c(0,+1L))
print(cnS)
points(cnS, pch=21, cex=1.2, lwd=2, col="purple")

legend("topright", pch=c(19, 21), col=c("#999999", "purple"),
       sprintf(c("raw [n=%d]", "CN in {0,1} [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnS))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Kernel smoothing stratified by state
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Kernel smoothing stratified by state w/ Gaussian kernel")

cnSa <- kernelSmoothingByState(cn, h=2)
points(cnSa, col="blue")

cnSb <- kernelSmoothingByState(cn, h=5)
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Binned smoothing stratified by state
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Binned smoothing stratified by state")

cnSa <- binnedSmoothingByState(cn, by=3, verbose=-1)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- binnedSmoothingByState(cn, by=9, verbose=-1)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")

The SegmentedGenomicSignalsInterface class interface

Description

Package: aroma.core
Class SegmentedGenomicSignalsInterface

Interface
~~|
~~+--SegmentedGenomicSignalsInterface

Directly known subclasses:
SegmentedAlleleBFractions, SegmentedCopyNumbers

public class SegmentedGenomicSignalsInterface
extends Interface

Usage

SegmentedGenomicSignalsInterface(...)

Arguments

...

Not used.

Fields and Methods

Methods:

	`as.data.frame`	-
	`binnedSmoothingByState`	-
	`extractSubsetByState`	-
	`findChangePointsByState`	-
	`getStateColorMap`	-
	`getStateColors`	-
	`getStates`	-
	`getUniqueStates`	-
	`kernelSmoothingByState`	-
	`plot`	-
	`points`	-
	`setStateColorMap`	-
	`setStates`	-

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The UnitAnnotationDataFile interface class

Description

Package: aroma.core
Class UnitAnnotationDataFile

Interface
~~|
~~+--UnitAnnotationDataFile

Directly known subclasses:
AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile, AromaUnitTabularBinaryFile, AromaUnitTypesFile, TextUnitNamesFile, UnitNamesFile, UnitTypesFile

public static class UnitAnnotationDataFile
extends Interface

A UnitAnnotationDataFile provides methods for querying certain types of chip type annotation data by units.

Usage

UnitAnnotationDataFile(...)

Arguments

...

Arguments passed to Interface.

Methods

Methods:

	`byChipType`	-
	`getAromaUflFile`	-
	`getAromaUgpFile`	-
	`getChipType`	-
	`getPlatform`	-
	`nbrOfUnits`	-

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The UnitNamesFile interface class

Description

Package: aroma.core
Class UnitNamesFile

Interface
~~|
~~+--UnitAnnotationDataFile
~~~~~~~|
~~~~~~~+--UnitNamesFile

Directly known subclasses:
TextUnitNamesFile

public abstract static class UnitNamesFile
extends UnitAnnotationDataFile

A UnitNamesFile provides methods for querying the unit names of a given chip type.

Usage

UnitNamesFile(...)

Arguments

...

Arguments passed to UnitAnnotationDataFile.

Methods

Methods:

	`getUnitNames`	-
	`indexOf`	-
	`nbrOfUnits`	-

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

The UnitTypesFile interface class

Description

Package: aroma.core
Class UnitTypesFile

Interface
~~|
~~+--UnitAnnotationDataFile
~~~~~~~|
~~~~~~~+--UnitTypesFile

Directly known subclasses:
AromaUnitTypesFile

public abstract static class UnitTypesFile
extends UnitAnnotationDataFile

A UnitTypesFile provides methods for querying the unit types of a given chip type, e.g. genotyping or copy-number unit, exon unit etc.

Usage

UnitTypesFile(...)

Arguments

...

Arguments passed to UnitAnnotationDataFile.

Methods

Methods:

	`getUnitTypes`	-
	`nbrOfUnits`	-

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from Interface:
extend, print, uses

The aroma unit-type map

unknown=0, expression=1, genotyping=2, resequencing=3, tag=4, copynumber=5, genotypingcontrol=6, expressioncontrol=7

Author(s)

Henrik Bengtsson

Creates a Grayscale (Color) Image from a matrix file

Description

Creates a Grayscale (Color) Image from a matrix file.

Usage

## S3 method for class 'matrix'
as.GrayscaleImage(z, transforms=NULL, interleaved=c("none", "h", "v", "auto"), scale=1,
  ..., verbose=FALSE)

Arguments

z

A KxN matrix.

transforms

A list of transform functions.

interleaved

A character string specifying how the image data should be interleaved, if at all.

scale

A numeric scale factor in (0,+Inf) for resizing the imaging. If 1, no resizing is done.

...

Passed to colorize() for the object created.

verbose

A logical or a Verbose object.

Value

Returns a bitmap image object.

Author(s)

Henrik Bengtsson, Ken Simpson

Binned smoothing of a matrix column by column

Description

Binned smoothing of a matrix column by column.

Usage

## S3 method for class 'matrix'
colBinnedSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=NULL, xOutRange=NULL,
  from=min(x, na.rm = TRUE), to=max(x, na.rm = TRUE), by=NULL, length.out=length(x),
  na.rm=TRUE, FUN="median", ..., verbose=FALSE)

Arguments

Y

A numeric JxI matrix (or a vector of length J.)

x

A (optional) numeric vector specifying the positions of the J entries. The default is to assume uniformly distributed positions.

w

A optional numeric vector of prior weights for each of the J entries.

xOut

Optional numeric vector of K bin center locations.

xOutRange

Optional Kx2 matrix specifying the boundary locations for K bins, where each row represents a bin [x0,x1). If not specified, the boundaries are set to be the midpoints of the bin centers, such that the bins have maximum lengths without overlapping. Vice verse, if xOut is not specified, then xOut is set to be the mid points of the xOutRange boundaries.

from, to, by, length.out

If neither xOut nor xOutRange is specified, the xOut is generated uniformly from these arguments, which specify the center location of the first and the last bin, and the distance between the center locations, utilizing the seq() function. Argument length.out can be used as an alternative to by, in case it specifies the total number of bins instead.

FUN

A function.

na.rm

If TRUE, missing values are excluded, otherwise not.

...

Not used.

verbose

See Verbose.

Details

Note that all zero-length bins [x0,x1) will get result in an NA value, because such bins contain no data points. This also means that colBinnedSmoothing(Y, x=x, xOut=xOut) where xOut contains duplicated values, will result in some zero-length bins and hence NA values.

Value

Returns a numeric KxI matrix (or a vector of length K) where K is the total number of bins. The following attributes are also returned:

xOut: The center locations of each bin.
xOutRange: The bin boundaries.
count: The number of data points within each bin (based solely on argument x).
binWidth: The average bin width.

Author(s)

Henrik Bengtsson

Examples

# Number of tracks
I <- 4

# Number of data points per track
J <- 100

# Simulate data with a gain in track 2 and 3
x <- 1:J
Y <- matrix(rnorm(I*J, sd=1/2), ncol=I)
Y[30:50,2:3] <- Y[30:50,2:3] + 3

# Uniformly distributed equal-sized bins
Ys3 <- colBinnedSmoothing(Y, x=x, from=2, by=3)
Ys5 <- colBinnedSmoothing(Y, x=x, from=3, by=5)

# Custom bins
xOutRange <- t(matrix(c(
  1, 11,
 11, 31,
 31, 41,
 41, 51,
 51, 81,
 81, 91,
 91,101
), nrow=2))
YsC <- colBinnedSmoothing(Y, x=x, xOutRange=xOutRange)

# Custom bins specified by center locations with
# maximized width relative to the neighboring bins.
xOut <- c(6, 21, 36, 46, 66, 86, 96)
YsD <- colBinnedSmoothing(Y, x=x, xOut=xOut)

xlim <- range(x)
ylim <- c(-3,5)
layout(matrix(1:I, ncol=1))
par(mar=c(3,3,1,1)+0.1, pch=19)
for (ii in 1:I) {
  plot(NA, xlim=xlim, ylim=ylim)
  points(x, Y[,ii], col="#999999")

  xOut <- attr(Ys3, "xOut")
  lines(xOut, Ys3[,ii], col=2)
  points(xOut, Ys3[,ii], col=2)

  xOut <- attr(Ys5, "xOut")
  lines(xOut, Ys5[,ii], col=3)
  points(xOut, Ys5[,ii], col=3)

  xOut <- attr(YsC, "xOut")
  lines(xOut, YsC[,ii], col=4)
  points(xOut, YsC[,ii], col=4, pch=15)

  xOut <- attr(YsD, "xOut")
  lines(xOut, YsD[,ii], col=5)
  points(xOut, YsD[,ii], col=5, pch=15)

  if (ii == 1) {
    legend("topright", pch=c(19,19,15,15), col=c(2,3,4,5),
           c("by=3", "by=5", "Custom #1", "Custom #2"), horiz=TRUE, bty="n")
  }
}


# Sanity checks
xOut <- x
YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut)
stopifnot(all(YsT == Y))
stopifnot(all(attr(YsT, "counts") == 1))

xOut <- attr(YsD, "xOut")
YsE <- colBinnedSmoothing(YsD, x=xOut, xOut=xOut)
stopifnot(all(YsE == YsD))
stopifnot(all(attr(YsE, "xOutRange") == attr(YsD, "xOutRange")))
stopifnot(all(attr(YsE, "counts") == 1))

# Scramble ordering of loci
idxs <- sample(x)
x2 <- x[idxs]
Y2 <- Y[idxs,,drop=FALSE]
Y2s <- colBinnedSmoothing(Y2, x=x2, xOut=x2)
stopifnot(all(attr(Y2s, "xOut") == x2))
stopifnot(all(attr(Y2s, "counts") == 1))
stopifnot(all(Y2s == Y2))

xOut <- x[seq(from=2, to=J, by=3)]
YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut)
stopifnot(all(YsT == Ys3))
stopifnot(all(attr(YsT, "counts") == 3))

xOut <- x[seq(from=3, to=J, by=5)]
YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut)
stopifnot(all(YsT == Ys5))
stopifnot(all(attr(YsT, "counts") == 5))

Kernel smoothing of a matrix column by column

Description

Kernel smoothing of a matrix column by column.

Usage

## S3 method for class 'matrix'
colKernelSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=x,
  kernel=c("gaussian", "uniform"), h, censorH=3, na.rm=TRUE, robust=FALSE, ...,
  verbose=FALSE)

Arguments

Y

A numeric JxI matrix (or a vector of length J.)

x

A (optional) numeric vector specifying the positions of the J entries. The default is to assume uniformly distributed positions.

w

A optional numeric vector of prior weights for each of the J entries.

xOut

A numeric vector specifying K target positions where the kernel is applied.

kernel

A character string or a function specifying the kernel used.

h

A single positive numeric specifying the bandwidth of the kernel.

censorH

A single positive numeric specifying the where to truncate the kernel. If Inf, no truncation is done.

na.rm

If TRUE, missing values are excluded, otherwise not.

robust

If TRUE, robust estimators are used, otherwise not.

...

Not used.

verbose

See Verbose.

Value

Returns a numeric KxI matrix (or a vector of length K).

Author(s)

Henrik Bengtsson

Examples

J <- 100
I <- 4
Y <- matrix(rnorm(I*J, sd=1/2), ncol=I)
# Introduce a gain in column 2 and 3
Y[30:50,2:3] <- Y[30:50,2:3] + 3
x <- 1:J

xOut <- x
Ys1 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=1)
Ys5 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=5)

xlim <- range(c(x,xOut))
ylim <- c(-3,5)
layout(matrix(1:I, ncol=1))
par(mar=c(3,3,1,1)+0.1, pch=19)
for (ii in 1:I) {
  plot(NA, xlim=xlim, ylim=ylim)
  points(x, Y[,ii], col="#999999")
  lines(xOut, Ys1[,ii], col=2)
  points(xOut, Ys1[,ii], col=2)
  lines(xOut, Ys5[,ii], col=3)
  points(xOut, Ys5[,ii], col=3)
}

Displays the explorer in the default browser

Description

Displays the explorer in the default browser.

Usage

## S3 method for class 'Explorer'
display(this, filename=sprintf("%s.html", class(this)[1]), ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Performs Circular Binary Segmentation (CBS) on a data set

Description

Performs Circular Binary Segmentation (CBS) on a data set for one or more chip types.

Usage

  ## Default S3 method:
doCBS(dataSet, tags=NULL, chipTypes, arrays=NULL, ..., verbose=FALSE)
  ## S3 method for class 'CopyNumberDataSet'
doCBS(ds, arrays=NULL, ...)
  ## S3 method for class 'CopyNumberDataSetTuple'
doCBS(dsTuple, arrays=NULL, ..., verbose=FALSE)

Arguments

ds, dsTuple, dataSet

A CopyNumberDataSet, a CopyNumberDataSetTuple or a character string with the name of one of them.

tags

An optional character vector of data set tags (only when dataSet is specified).

chipTypes

A character vector specifying the chip types for the different data sets (only when dataSet is specified).

arrays

An optional vector specifying the subset of arrays to process.

...

Additional arguments passed to CbsModel and its fit() method.

verbose

A logical or Verbose.

Value

Returns the output dataset of CbsModel.

Author(s)

Henrik Bengtsson

Examples

## Not run: 
 
dataSet <- "GSE20939"
tags <- "ACC,-XY,BPN,-XY,RMA,FLN,-XY"
chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
fit <- doCBS(dataSet, tags=tags, chipTypes=chipTypes, verbose=-10)
print(fit)


## End(Not run)

Download a particular chip type annotation file

Description

Download a particular chip type annotation file by its chip type, tags and suffix.

Usage

## S3 method for class 'AromaRepository'
downloadChipTypeFile(this, chipType, tags=NULL, suffix=sprintf(".%s", ext), ext=NULL,
  ..., gunzip=TRUE, skip=TRUE, overwrite=FALSE, mustExist=TRUE, verbose=getVerbose(this))

Arguments

chipType

The chip type of the file to be downloaded.

tags

Optional tags of the file to be downloaded.

suffix

The filename suffix (including any preceding period) of the file to be downloaded.

ext

The filename extension.

...

Additional arguments passed to *downloadFile().

skip

If TRUE, an already downloaded file is skipped.

overwrite

If TRUE, an not skipping, an already downloaded file is overwritten, otherwise an error is thrown.

mustExist

If TRUE, an exception is thrown if no file matching is available either locally or on the repository.

verbose

See Verbose.

Value

Returns the relative pathname of the uncompressed downloaded file.

Author(s)

Henrik Bengtsson

Download a particular file from the repository

Description

Download a particular file from the repository by its relative pathname.

Usage

## S3 method for class 'AromaRepository'
downloadFile(this, filename, path=NULL, caseSensitive=FALSE, gzipped=TRUE, skip=TRUE,
  overwrite=FALSE, ..., verbose=getVerbose(this))

Arguments

filename, path

The filename and the relative path of the file to be download.

gzipped

If TRUE, a gzipped file is downloaded and decompressed.

skip

If TRUE, an already downloaded file is skipped.

overwrite

If TRUE, an not skipping, an already downloaded file is overwritten, otherwise an error is thrown.

...

Additional arguments passed to downloadFile.

verbose

See Verbose.

Value

Returns the pathname of the uncompressed downloaded file.

Author(s)

Henrik Bengtsson

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

Description

Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly using a first-order difference variance estimator, which is an estimator that is fairly robust for change points.

Usage

## S3 method for class 'CopyNumberChromosomalModel'
estimateSds(this, arrays=seq_len(nbrOfArrays(this)), chromosomes=getChromosomes(this),
  ..., verbose=FALSE)

Arguments

arrays

The arrays to be queried.

chromosomes

The chromosomes to be queried.

...

Additional arguments passed to *extractRawCopyNumbers().

verbose

See Verbose.

Value

Returns a CxK double matrix where C is the number of chromosomes, and K is the number of arrays (arrays are always the last dimension).

Author(s)

Henrik Bengtsson

Estimates the standard deviation of the raw Ys

Description

Estimates the standard deviation of the raw Ys robustly or non-robustly using either a "direct" estimator or a first-order difference estimator.

Usage

## S3 method for class 'RawGenomicSignals'
estimateStandardDeviation(this, field=NULL, method=c("diff", "direct"),
  estimator=c("mad", "sd"), na.rm=TRUE, weights=getWeights(this), ...)

Arguments

field

A character specifying the field to estimate.

method

If "diff", the estimate is based on the first-order contiguous differences of raw Ys. If "direct", it is based directly on the raw Ys.

estimator

If "mad", the robust mad estimator is used. If "sd", the sd estimator is used.

na.rm

If TRUE, missing values are excluded first.

weights

Locus specific weights.

...

Not used.

Value

Returns a non-negative numeric value.

Author(s)

Henrik Bengtsson

Export total and allele B signal data sets as a unified parent-specific copy number signal data set

Description

Export total and allele B signal data sets as a unified parent-specific copy number signal data set, where each sample is stored in one data file (contrary to the input data sets where each sample is stored in two separated files).

Usage

 ## S3 method for class 'AromaUnitTotalCnBinarySet'
exportAromaUnitPscnBinarySet(dsT, dsB="*", dataSet="*", tags="*", ...,
  rootPath="totalAndFracBData/", overwrite=!skip, skip=TRUE, verbose=FALSE)
 ## S3 method for class 'list'
exportAromaUnitPscnBinarySet(dsList, ...)

Arguments

dsT, dsB

An AromaUnitTotalCnBinarySet and an AromaUnitFracBCnBinarySet with coupled sets of samples that match up by name. If they don't match up, an exception is thrown. The allele B fraction (BAF) data set dsB is by default inferred from the total CN data set dsT.

dataSet, tags

The name and tags of the output data set. The default is to infer those from the input dsT data set.

...

Not used.

rootPath

The root path of the output data set.

overwrite, skip

Specifies whether to overwrite and/or skip already exported samples.

verbose

See Verbose.

Value

Returns an AromaUnitPscnBinarySet object.

Allele-specific CRMAv2 pipeline

A common use case is to run allele-specific CRMAv2, e.g. dsNList <- doASCRMAv2(csR), which outputs a list dsNList with elements corresponding to dsT and dsB. This output can be exported to AromaUnitPscnBinarySet by this method as dsN <- exportAromaUnitPscnBinarySet(dsNList).

Author(s)

Henrik Bengtsson

Extracts relative copy numbers

Description

Extracts relative copy numbers for a particular array and chromosome.

Usage

## S3 method for class 'CopyNumberChromosomalModel'
extractRawCopyNumbers(this, array, chromosome, ..., logBase=2, cache=FALSE, force=FALSE,
  verbose=FALSE)

Arguments

array

The index of the array to be extracted.

chromosome

The index of the chromosome to be extracted.

...

See subclasses.

logBase

(optional) The base of the logarithm used for the ratios. If NULL, the ratios are not logged.

cache

If TRUE, results are cached, otherwise not.

force

If TRUE, cached results are ignored.

verbose

See Verbose.

Value

See subclasses.

Parallel processing

Except for an in-object caching (cache=TRUE), this method access data solely in an read-only fashion. This method is safe to call with different arrays and/or chromosomes in parallel.

Author(s)

Henrik Bengtsson

Locates an annotation data file

Description

Locates an annotation data file.

Usage

## Default S3 method:
findAnnotationData(name=NULL, tags=NULL, set, pattern=NULL, private=FALSE,
  escapes=c("+"), ..., firstOnly=TRUE, paths=NULL, verbose=FALSE)

Arguments

name

Optional character string.

tags

Optional character string. Only used if argument pattern is not specified.

pattern

A filename pattern to search for. If NULL, then defaults to the fullname as defined by arguments name and tags.

private

If FALSE, files and directories starting with a periods are ignored.

escapes

A character vector specify symbols to be escaped in argument pattern.

...

Arguments passed to findFiles.

firstOnly

If TRUE, only the first matching pathname is returned.

paths

A character vector of paths to search. If NULL, default paths are used.

set

A character string specifying what type of annotation to search for.

verbose

A logical or Verbose.

Value

Returns NULL, one or several matching pathnames.

Author(s)

Henrik Bengtsson

Locates an annotation data file by its chip type

Description

Locates an annotation data file by its chip type.

Usage

## Default S3 method:
findAnnotationDataByChipType(chipType, pattern=chipType, ...)

Arguments

chipType

A character string.

pattern

A filename pattern to search for.

...

Arguments passed to findAnnotationData().

Author(s)

Henrik Bengtsson

Finds files in the data set still not processed

Description

Finds files in the data set still not processed.

Usage

## S3 method for class 'AromaTransform'
findFilesTodo(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns a named integer vector specifying the indices of the files still not processed.

Author(s)

Henrik Bengtsson

Fits the model

Description

Fits the model.

Usage

## S3 method for class 'CopyNumberChromosomalModel'
fit(...)

Arguments

...

See subclasses.

Value

See subclasses.

Author(s)

Henrik Bengtsson

Fits the model

Description

Fits the model.

Usage

## S3 method for class 'CopyNumberSegmentationModel'
fit(this, arrays=NULL, chromosomes=getChromosomes(this), force=FALSE, ...,
  .retResults=FALSE, verbose=FALSE)

Arguments

arrays

A vector of array indices specifying which arrays to be considered. If NULL, all are processed.

chromosomes

A vector of chromosomes indices specifying which chromosomes to be considered. If NULL, all are processed.

force

If FALSE, the model will not be fitted again if it was already fitted.

...

Additional arguments passed to the segmentation method for the RawGenomicSignals.

.retResults

If TRUE, the segmentation fit structures are returned for each fitted array and chromosome.

verbose

A logical or Verbose.

Value

Returns a named list of named lists.

Additional arguments to the internal fit function

Arguments in ... are passed down to the internal fit function, which means that it is possible to fine tune even further.

Author(s)

Henrik Bengtsson

Fits an affine transformation to allele A and allele B data

Description

Fits an affine transformation to allele A and allele B data using robust estimators.

Usage

## S3 method for class 'matrix'
fitGenotypeCone(y, flavor=c("sfit", "expectile"), ...)

Arguments

y

A numeric Nx2 matrix with one column for each allele and where N is the number of data points.

flavor

A character string specifying what model/algorithm should be used to fit the genotype cone.

...

Additional arguments passed to the internal fit function.

Value

Returns a named list structure.

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fit genotype cone based on available methods (==packages)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
flavors <- c("expectile", "sfit")
## The 'expectile' package does not do proper S3 registration
if (getRversion() >= "3.6.0") flavors <- setdiff(flavors, "expectile")
keep <- sapply(flavors, FUN=require, character.only=TRUE)
flavors <- flavors[keep]
cat("Available fitting flavors:", paste(flavors, collapse=", "), "\n")
hasSfit <- is.element("sfit", flavors)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulate data (taken from the cfit.matrix() example of 'sfit')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#set.seed(0xbeef)

N <- 1000

# Simulate genotypes
g <- sample(c("AA", "AB", "AB", "BB"), size=N, replace=TRUE)

# Simulate concentrations of allele A and allele B
X <- matrix(rexp(N), nrow=N, ncol=2)
colnames(X) <- c("A", "B")
X[g == "AA", "B"] <- 0
X[g == "BB", "A"] <- 0
X[g == "AB",] <- X[g == "AB",] / 2

# Transform noisy X
xi <- matrix(rnorm(2*N, mean=0, sd=0.05), ncol=2)
a0 <- c(0,0)+0.3
A <- matrix(c(0.9, 0.1, 0.1, 0.8), nrow=2, byrow=TRUE)
A <- apply(A, MARGIN=2, FUN=function(u) u / sqrt(sum(u^2)))
Z <- t(a0 + A %*% t(X + xi))

# Add noise to Y
eps <- matrix(rnorm(2*N, mean=0, sd=0.05), ncol=2)
Y <- Z + eps


lim <- c(-1/2,6)
xlab <- "Allele A"
ylab <- "Allele B"
plot(Y, xlab=xlab, ylab=ylab, xlim=lim, ylim=lim)
lines(x=c(0,0,2*lim[2]), y=c(2*lim[2],0,0), col="#aaaaaa", lwd=3, lty=3)

# Different alpha sequences to illustrate the impact
alphas <- c(0.075, 0.05, 0.01, 0.03, 0.002, 0.001)

cols <- seq(from=2, to=length(alphas)+1)
legend("topright", sprintf("%.3f", alphas), col=cols, lwd=4, title="Alphas")

for (kk in seq_along(alphas)) {
  for (flavor in flavors) {
    fit <- fitGenotypeCone(Y, alpha=alphas[kk], flavor=flavor)
    YN <- backtransformGenotypeCone(Y, fit=fit)
    if (hasSfit) {
      radials(fit$M, lwd=3, col=cols[kk], lty=ifelse(flavor == "sfit", 1,2))
      drawApex(fit$M, col=cols[kk], pch=19, cex=2)
    }
    points(YN, col=cols[kk])
  }
}
lines(x=c(0,0,2*lim[2]), y=c(2*lim[2],0,0), col="#aaaaaa", lwd=3, lty=3)

Fits an affine transformation to allele A and allele B data

Description

Fits an affine transformation to allele A and allele B data using robust estimators.

Usage

## S3 method for class 'matrix'
fitGenotypeConeBySfit(y, alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, ...)

Arguments

y

A numeric Nx2 matrix with one column for each allele and where N is the number of data points.

alpha

A numeric vector of decreasing values in (0,1). This parameter "determines how far we are willing to press the boundary of the [genotype cone]". Lowering alpha expand the cone. When alpha goes to zero, all data points will be on or inside the cone.

q, Q

Percentiles in [0,100] for which data points that are below (above) will be assigned zero weight in the fitting of the parameters.

...

Additional arguments passed to the cfit() of the sfit package.

Value

Returns the parameter estimates as a named list with elements:

M

An estimate of the three vertices defining the genotype triangle. These three vertices are describes as an 2x3 matrix with column origin, AA, and BB.

Minv

The inverse of M.

origin

The estimate of the shift.

W

The estimate of shear/rotation matrix with columns AA and BB.

Winv

The inverse of W.

params

The parameters used for the fit, i.e. alpha, q, Q, and those passed in ....

dimData

The dimension of the input data.

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fit genotype cone based on available methods (==packages)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
flavors <- c("expectile", "sfit")
## The 'expectile' package does not do proper S3 registration
if (getRversion() >= "3.6.0") flavors <- setdiff(flavors, "expectile")
keep <- sapply(flavors, FUN=require, character.only=TRUE)
flavors <- flavors[keep]
cat("Available fitting flavors:", paste(flavors, collapse=", "), "\n")
hasSfit <- is.element("sfit", flavors)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulate data (taken from the cfit.matrix() example of 'sfit')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#set.seed(0xbeef)

N <- 1000

# Simulate genotypes
g <- sample(c("AA", "AB", "AB", "BB"), size=N, replace=TRUE)

# Simulate concentrations of allele A and allele B
X <- matrix(rexp(N), nrow=N, ncol=2)
colnames(X) <- c("A", "B")
X[g == "AA", "B"] <- 0
X[g == "BB", "A"] <- 0
X[g == "AB",] <- X[g == "AB",] / 2

# Transform noisy X
xi <- matrix(rnorm(2*N, mean=0, sd=0.05), ncol=2)
a0 <- c(0,0)+0.3
A <- matrix(c(0.9, 0.1, 0.1, 0.8), nrow=2, byrow=TRUE)
A <- apply(A, MARGIN=2, FUN=function(u) u / sqrt(sum(u^2)))
Z <- t(a0 + A %*% t(X + xi))

# Add noise to Y
eps <- matrix(rnorm(2*N, mean=0, sd=0.05), ncol=2)
Y <- Z + eps


lim <- c(-1/2,6)
xlab <- "Allele A"
ylab <- "Allele B"
plot(Y, xlab=xlab, ylab=ylab, xlim=lim, ylim=lim)
lines(x=c(0,0,2*lim[2]), y=c(2*lim[2],0,0), col="#aaaaaa", lwd=3, lty=3)

# Different alpha sequences to illustrate the impact
alphas <- c(0.075, 0.05, 0.01, 0.03, 0.002, 0.001)

cols <- seq(from=2, to=length(alphas)+1)
legend("topright", sprintf("%.3f", alphas), col=cols, lwd=4, title="Alphas")

for (kk in seq_along(alphas)) {
  for (flavor in flavors) {
    fit <- fitGenotypeCone(Y, alpha=alphas[kk], flavor=flavor)
    YN <- backtransformGenotypeCone(Y, fit=fit)
    if (hasSfit) {
      radials(fit$M, lwd=3, col=cols[kk], lty=ifelse(flavor == "sfit", 1,2))
      drawApex(fit$M, col=cols[kk], pch=19, cex=2)
    }
    points(YN, col=cols[kk])
  }
}
lines(x=c(0,0,2*lim[2]), y=c(2*lim[2],0,0), col="#aaaaaa", lwd=3, lty=3)

Fits an affine transformation to multi-dimensional data

Description

Fits an affine transformation to multi-dimensional data using robust estimators.

Usage

## S3 method for class 'matrix'
fitMultiDimensionalCone(y, alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, ...,
  flavor=c("sfit", "expectile"))

Arguments

y

A numeric NxK matrix with one column for each dimension and where N is the number of data points.

alpha

q, Q

Percentiles in [0,100] for which data points that are below (above) will be assigned zero weight in the fitting of the parameters.

...

Additional arguments passed to the cfit() function of the sfit package.

flavor

A character string specifying what model/algorithm should be used to fit the genotype cone.

Value

Returns the parameter estimates as a named list with elements:

M

An estimate of the three vertices defining the genotype triangle. These three vertices are describes as an 2x3 matrix with column origin, AA, and BB.

Minv

The inverse of M.

origin

The estimate of the shift.

W

The estimate of shear/rotation matrix with columns AA and BB.

Winv

The inverse of W.

params

The parameters used for the fit, i.e. alpha, q, Q, and those passed in ....

dimData

The dimension of the input data.

Author(s)

Henrik Bengtsson

Examples

if (require("sfit")) {
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulate data (taken from the cfit.matrix() example of 'sfit')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
N <- 1000

# Simulate sequences
nucleotides <- c("A", "C", "G", "T")
g <- sample(nucleotides, size=N, replace=TRUE)
ndim <- length(nucleotides)

# Simulate concentrations of allele A and allele B
X <- matrix(rexp(N), nrow=N, ncol=ndim)
colnames(X) <- nucleotides
for (nucleotide in nucleotides) {
  cc <- match(nucleotide, nucleotides)
  X[g == nucleotide, -cc] <- 0
}

# The true offset
a0 <- rep(0.3, times=ndim)

# The crosstalk matrix
A <- matrix(c(
  0.9, 0.3, 0.2, 0.1,
  0.1, 0.8, 0.1, 0.1,
  0.3, 0.4, 0.7, 0.1,
  0.1, 0.1, 0.6, 0.9
), nrow=ndim, byrow=TRUE)
A <- apply(A, MARGIN=2, FUN=function(u) u / sqrt(sum(u^2)))

# Simulate random errors on the input
xi <- matrix(rnorm(ndim*N, mean=0, sd=0.05), ncol=ndim)

# Generate the noisy crosstalk affected input data
Z <- t(a0 + A %*% t(X + xi))

# Generate the noisy observations of the latter
eps <- matrix(rnorm(ndim*N, mean=0, sd=0.05), ncol=ndim)
Y <- Z + eps

# Fit crosstalk model and calibrate data accordingly
fit <- fitMultiDimensionalCone(Y, flavor="sfit")
Yc <- backtransformMultiDimensionalCone(Y, fit=fit)

lim <- c(-0.5,6)
layout(matrix(c(1,2,3,0,4,5,0,0,6), nrow=3, ncol=3, byrow=TRUE))
par(mar=c(5,4,1,1)+0.1)
for (ii in 1:(ndim-1)) {
  for (jj in (ii+1):ndim) {
    cc <- c(jj,ii)
    labs <- nucleotides[cc]
    plot(Y[,cc], cex=0.8, xlim=lim, ylim=lim, xlab=labs[1], ylab=labs[2])
    points(Yc[,cc], cex=0.8, col="blue")
    Mcc <- fit$M[c(1,1+cc),cc]
    class(Mcc) <- class(fit$M)
    lines(Mcc, lwd=2, col="red")
  }
}

}

Gets the alias of the output set

Description

Gets the alias of the output set.

Usage

## S3 method for class 'Explorer'
getAlias(this, ...)

Arguments

...

Not used.

Value

Returns a character, or NULL if no alias is set.

Author(s)

Henrik Bengtsson

Gets the platform

Description

Gets the platform object.

Usage

## S3 method for class 'AromaPlatformInterface'
getAromaPlatform(this, ..., force=FALSE)

Arguments

...

Not used.

force

If TRUE, any cached results are ignored, otherwise not.

Value

Returns an AromaPlatform object.

Author(s)

Henrik Bengtsson

Gets a list of cache key items

Description

Gets a list of cache key items that will be added to other cache key items used to generate the cache key.

Usage

## S3 method for class 'CacheKeyInterface'
getCacheKey(this, ...)

Arguments

...

Additional named arguments to be appended to the list of key items.

Details

The default list of cache key items are:

the class name of the object as a character string.

Classes extending/implementing this Interface may override these items.

Value

Returns a list of cache items.

Author(s)

Henrik Bengtsson

Gets a list of cache key items

Description

Gets a list of cache key items that will be added to other cache key items used to generate the cache key.

Usage

## S3 method for class 'FileCacheKeyInterface'
getCacheKey(this, ...)

Arguments

...

Additional named arguments to be appended to the list of key items.

Details

The default list of cache key items are:

the class name of the object as a character string.
the file name (aka the basename) as a character string.
the file size as a numeric scalar.
the file checksum as a character string.

Classes extending/implementing this Interface may override these items.

Value

Returns a list of cache items.

Author(s)

Henrik Bengtsson

Gets the chip type

Description

Gets the chip type.

Usage

## S3 method for class 'AromaPlatformInterface'
getChipType(...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets a label for all chip types merged

Description

Gets a label for all chip types merged.

Usage

## S3 method for class 'ChromosomalModel'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the chromosomes to be processed

Description

Gets the chromosomes to be processed.

Usage

## S3 method for class 'ChromosomalModel'
getChromosomes(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets the chromosomes available

Description

Gets the chromosomes available.

Usage

## S3 method for class 'ChromosomeExplorer'
getChromosomes(this, ...)

Arguments

...

Not used.

Value

Returns a integer vector.

Author(s)

Henrik Bengtsson

Gets the full name of the output data set

Description

Gets the full name of the output data set, which is the name with comma separated tags.

Usage

## S3 method for class 'AromaTransform'
getFullName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the input data set

Description

Gets the input data set that is to be (or has been) transformed.

Usage

## S3 method for class 'AromaTransform'
getInputDataSet(this, ...)

Arguments

...

Not used.

Value

Returns an AromaMicroarrayDataSet.

Author(s)

Henrik Bengtsson

Gets the model

Description

Gets the model for which the explorer is displaying it results.

Usage

## S3 method for class 'ChromosomeExplorer'
getModel(this, ...)

Arguments

...

Not used.

Value

Returns a CopyNumberChromosomalModel.

Author(s)

Henrik Bengtsson

Gets the name of the output data set

Description

Gets the name of the output data set, which is the same as the input data set.

Usage

## S3 method for class 'AromaTransform'
getName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the name of the explorer

Description

Gets the name of the explorer, which is the same as the name of the data set.

Usage

## S3 method for class 'Explorer'
getName(this, ...)

Arguments

...

Not used.

Details

If a name alias has not been set explicitly, the name of the data set will used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the names of the arrays

Description

Gets the names of the arrays available to the model.

Usage

## S3 method for class 'ChromosomalModel'
getNames(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets the names of the input samples

Description

Gets the names of the input samples for which the explorer is displaying results.

Usage

## S3 method for class 'Explorer'
getNames(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets the transformed data set

Description

Gets the transformed data set, if processed.

Usage

## S3 method for class 'AromaTransform'
getOutputDataSet(this, onMissing=c("dropall", "drop", "NA", "error"), ...,
  incomplete=FALSE, className=NULL, force=FALSE, verbose=FALSE)

Arguments

...

Arguments passed to static method byPath() of the class of the input AromaMicroarrayDataSet.

onMissing

A character string specifying how non-processed files should be returned. If "drop", they are ignored and not part of the returned data set. If "dropall", NULL is returned unless all files are processed. If "NA", they are represented as a "missing" file. If "error", they are not accepted and an exception is thrown.

incomplete

[DEPRECATED] If the output data set is incomplete, then NULL is returned unless incomplete is TRUE.

force

If TRUE, any in-memory cached results are ignored.

verbose

See Verbose.

Value

Returns an AromaMicroarrayDataSet or NULL.

Author(s)

Henrik Bengtsson

Gets a list of parameters

Description

Gets a list of parameters associated with the object.

Usage

## S3 method for class 'ParametersInterface'
getParameters(this, ...)

Arguments

...

Not used.

Value

Returns a named list.

Author(s)

Henrik Bengtsson

Gets the parameters as character

Description

Gets the parameters as character.

Usage

## S3 method for class 'ParametersInterface'
getParametersAsString(this, ..., collapse=c(", ", "; "), drop=TRUE)

Arguments

...

Arguments passed to *getParameters().

collapse

(optional) A character string used to collapse the individual parameter strings.

drop

If TRUE and there is only one set of parameters, then a single character vector is returned, otherwise a list.

Value

Returns a list of character vectors, or a character vector.

Author(s)

Henrik Bengtsson

Gets the path of the output directory

Description

Gets the path of the output directory.

Usage

## S3 method for class 'AromaTransform'
getPath(this, create=TRUE, ...)

Arguments

create

If TRUE, the path is created, otherwise not.

...

Not used.

Details

Windows Shortcut links are recognized.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the path of the output directory

Description

Gets the path of the output directory.

Usage

## S3 method for class 'Explorer'
getPath(...)

Arguments

...

Not used.

Details

Windows Shortcut links are recognized.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the platform

Description

Gets the platform label.

Usage

## S3 method for class 'AromaPlatformInterface'
getPlatform(...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the root path of the output directory

Description

Gets the root path of the output directory that is returned by *getPath(). A root path is a directory in the current working directory.

Usage

## S3 method for class 'AromaTransform'
getRootPath(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the root path of the output directory

Description

Gets the root path of the output directory that is returned by *getPath(). A root path is a directory in the current working directory.

Usage

## S3 method for class 'Explorer'
getRootPath(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the tags of the output data set

Description

Gets the tags of the output data set, which equals the tags of the input data set plus the tags of this transformation.

Usage

## S3 method for class 'AromaTransform'
getTags(this, collapse=NULL, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets the tags of the explorer

Description

Gets the tags of the explorer, which are the tags of the data set plus additional tags.

Usage

## S3 method for class 'Explorer'
getTags(this, collapse=NULL, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets a unit annotation data file of a particular class

Description

Gets a unit annotation data file of a particular class for this AromaPlatformInterface.

Usage

## S3 method for class 'AromaPlatformInterface'
getUnitAnnotationDataFile(this, ..., className, force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to byChipType() for the class of interest.

className

A character string specifying the class of interest.

force

If TRUE, any cached results are ignored, otherwise not.

verbose

The Verbose to be used during processing.

Value

Returns TRUE if compatible and FALSE otherwise.

Author(s)

Henrik Bengtsson

Gets the indices of units by their names

Description

Gets the indices of units by their names.

Usage

## S3 method for class 'UnitNamesFile'
indexOf(this, pattern=NULL, names=NULL, ...)

Arguments

pattern

A pattern to be used for identifying unit names of interest. If NULL, no regular expression matching is done.

names

Names to be match exactly to the unit names.

...

Not used.

Value

Returns a vector of integers in [1,N] where N is the number of units in the underlying annotation chip type file.

Author(s)

Henrik Bengtsson

Checks if a particular unit annotation data file is compatible

Description

Checks if a particular unit annotation data file is compatible with this AromaPlatformInterface class.

Usage

## S3 method for class 'AromaPlatformInterface'
isCompatibleWith(this, udf, ...)

Arguments

udf

An unit annotation data file.

...

Not used.

Value

Returns TRUE if compatible and FALSE otherwise.

Author(s)

Henrik Bengtsson

Checks if the data set is processed or not

Description

Checks if the data set is processed or not.

Usage

## S3 method for class 'AromaTransform'
isDone(this, ...)

Arguments

...

Arguments passed to *findFilesTodo().

Value

Returns TRUE if the data set is processed, otherwise FALSE.

Author(s)

Henrik Bengtsson

Retrieves the files available on the repository under a particular path

Description

Retrieves the files available on the repository under a particular path.

Usage

## S3 method for class 'AromaRepository'
listFiles(this, path=NULL, full=TRUE, orderBy=c("name", "time"), ..., force=FALSE,
  verbose=getVerbose(this))

Arguments

path

The relative path to be listed.

orderBy

A character specifying how the returns files should be ordered.

...

Additional arguments passed to downloadFile.

force

If TRUE, cached results are redownloaded, otherwise not.

Details

Note that this method makes strong assumptions of the format of the downloaded HTML index file.

Value

Returns the relative pathnames of the files available.

Author(s)

Henrik Bengtsson

Applies a polishing function to blocks of rows and columns repeatedly

Description

Applies a polishing function to blocks of rows and columns repeatedly.

Usage

## S3 method for class 'matrix'
matrixBlockPolish(z, x=NULL, blockSizes=c(1, 1), FUN, ..., tol=0.01, maxIter=10,
  returnEffects=FALSE)

Arguments

z

A numeric KxN matrix.

x

A optional KxNx2 array (or KxN matrix).

blockSizes

A positive integer vector of length two.

FUN

A function taking numeric arguments z and x and returns a numeric object with either a scalar or the same number of elements as in z.

...

Additional arguments passed to the FUN function.

tol

A positive threshold specifying when the algorithm has converged.

maxIter

The maximum number of iterations.

returnEffects

If TRUE, the row and column effects are returned, otherwise not.

Value

Returns a named list.

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example 1: median polish
# From example(medpolish) in the 'stats' package
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

# Deaths from sport parachuting;  from ABC of EDA, p.224:
deaths <- matrix(c(14,15,14, 7,4,7, 8,2,10, 15,9,10, 0,2,0), ncol=3, byrow=TRUE)
rownames(deaths) <- c("1-24", "25-74", "75-199", "200++", "NA")
colnames(deaths) <- 1973:1975
print(deaths)

fit1 <- medpolish(deaths, trace=FALSE)
r1 <- residuals(fit1)
fit2 <- matrixBlockPolish(deaths, FUN=function(y, x, ...) median(y, ...))
r2 <- residuals(fit2)
stopifnot(all.equal(r1,r2))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example 2: smooth spline polish ("spatial smoothing")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# From example(image) in 'graphics' package
x <- y <- seq(-4*pi, 4*pi, len=27)
r <- sqrt(outer(x^2, y^2, FUN="+"))
z <- cos(r^2) * exp(-r/6)

fit <- matrixBlockPolish(z, FUN=function(z, x, ...) median(z, ...),
                                                      returnEffects=TRUE)
r1 <- residuals(fit)

fit <- matrixBlockPolish(z, FUN=function(z, x, ...) {
  fit <- smooth.spline(x=x, y=z, ...)
  predict(fit, x=x)$y
}, spar=0.25)
r2 <- residuals(fit)
print(range(r2))
image(r2)

Merges a list of boxplot.stats() elements

Description

Merges a list of boxplot.stats() elements.

Usage

## S3 method for class 'list'
mergeBoxplotStats(stats, ...)

Arguments

stats

A list of elements each in a format returned by boxplot.stats.

...

Not used.

Value

Returns a list structure in a format that is returned by boxplot.

Author(s)

Henrik Bengtsson

Examples

library("stats")

x <- matrix(rnorm(1000), ncol=5)
x <- as.data.frame(x)

stats0 <- boxplot(x, plot=FALSE)
stats1 <- lapply(x, FUN=boxplot.stats)
stats1b <- mergeBoxplotStats(stats1)
stopifnot(all.equal(stats0, stats1b))

bxp(stats1b)

Gets the number of arrays

Description

Gets the number of arrays used in the model.

Usage

## S3 method for class 'ChromosomalModel'
nbrOfArrays(this, ...)

Arguments

...

Not used.

Value

Returns an integer.

Author(s)

Henrik Bengtsson

Gets the total number of arrays

Description

Gets the total number of arrays considered by the explorer.

Usage

## S3 method for class 'Explorer'
nbrOfArrays(this, ...)

Arguments

...

Not used.

Value

Returns an integer.

Author(s)

Henrik Bengtsson

Gets the number of chip types

Description

Gets the number of chip types used in the model.

Usage

## S3 method for class 'AromaMicroarrayDataSetTuple'
nbrOfChipTypes(this, ...)

Arguments

...

Not used.

Value

Returns an integer.

Author(s)

Henrik Bengtsson

Gets the number of chip types

Description

Gets the number of chip types used in the model.

Usage

## S3 method for class 'ChromosomalModel'
nbrOfChipTypes(this, ...)

Arguments

...

Not used.

Value

Returns an integer.

Author(s)

Henrik Bengtsson

Plots parental specific copy numbers along the genome

Description

Plots parental specific copy numbers along the genome for one or more chromosomes. It is possible to specify what type of tracks to plot. Each type of track is plotted in its own panel.

Usage

## S3 method for class 'PairedPSCNData'
plotTracks(x, tracks=c("tcn", "dh", "tcn,c1,c2", "tcn,c1", "tcn,c2", "c1,c2", "betaN",
  "betaT", "betaTN")[1:3], pch=".", col=NULL, cex=1, grid=FALSE, xlim=NULL, Clim=c(0, 6),
  Blim=c(0, 1), xScale=1e-06, ..., add=FALSE, subplots=!add && (length(tracks) > 1),
  verbose=FALSE)

Arguments

tracks

A character vector specifying what types of tracks to plot.

pch

The type of the scatter points, if any.

col

The color of the scatter points, if any.

cex

The size of the scatter points, if any.

grid

If TRUE, horizontal lines are displayed.

xlim

(Optional) The genomic range to plot.

Clim

The range of copy numbers.

Blim

The range of allele B fractions (BAFs) and decrease of heterozygosity (DHs).

xScale

The scale factor used for genomic positions.

...

Not used.

add

If TRUE, the panels plotted are added to the existing plot, otherwise a new plot is created.

subplots

If TRUE, then subplots are automatically setup.

verbose

See Verbose.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Processes the data set

Description

Processes the data set.

Usage

## S3 method for class 'AromaTransform'
process(...)

Arguments

...

Not used.

Value

Returns a double vector.

Author(s)

Henrik Bengtsson

Generates image files, scripts and dynamic pages for the explorer

Description

Generates image files, scripts and dynamic pages for the explorer.

Usage

## S3 method for class 'ChromosomeExplorer'
process(this, arrays=NULL, chromosomes=NULL, ..., zooms=getZooms(this), layers=FALSE,
  verbose=FALSE)

Arguments

arrays

A vector of arrays specifying which arrays to be considered. If NULL, all are processed.

chromosomes

A vector of chromosomes specifying which chromosomes to be considered. If NULL, all are processed.

...

Not used.

verbose

A logical or Verbose.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Generates image files, scripts and dynamic pages for the explorer

Description

Generates image files, scripts and dynamic pages for the explorer.

Usage

## S3 method for class 'Explorer'
process(...)

Arguments

...

Not used.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

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

Description

Gets the running time of the R process and its children processes. This function is a safe wrapper for proc.time(), which might not exist on all platforms. It "determines how much time (in seconds) the currently running R process already consumed". In addition it adds descriptive names of the returned values. For more details, see proc.time().

Usage

## Default S3 method:
processTime(since=NULL, units=c("seconds", "milliseconds", "minutes", "hours", "days"),
  fmtstr=NULL, ...)

Arguments

since

An optional numeric vector to be subtracted from the value of proc.time(). This is useful for calculating "lap times".

units

A character string specifying the unit of the returned values.

fmtstr

If given, a format string to convert the times to strings via sprintf().

...

Not used.

Value

Returns a named numeric vector of length 5. For more details, see proc.time().

Author(s)

Henrik Bengtsson

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

Description

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

Usage

## S3 method for class 'AromaTabularBinaryFile'
readFooter(this, asXmlString=FALSE, ...)

Arguments

asXmlString

If TRUE, the file footer is returned as a character string.

...

Not used.

Value

Returns a named list structure (or a character string).

Author(s)

Henrik Bengtsson

Segment copy numbers using the CBS method

Description

Segment copy numbers using the CBS method of the DNAcopy package. For more details on the Circular Binary Segmentation (CBS) method see [1,2].

Usage

## S3 method for class 'RawGenomicSignals'
segmentByCBS(this, ..., seed=NULL, cache=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to the segmentation function.

seed

An (optional) integer specifying the random seed to be set before calling the segmentation method. The random seed is set to its original state when exiting. If NULL, it is not set.

cache

If TRUE, results are cached to file, otherwise not.

force

If TRUE, cached results are ignored.

verbose

See Verbose.

Details

Internally segment is used to segment the signals. This segmentation method support weighted segmentation.

The "DNAcopy::segment" implementation of CBS uses approximation through random sampling for some estimates. Because of this, repeated calls using the same signals may result in slightly different results.

Value

Returns the fit object.

Author(s)

Henrik Bengtsson

References

[1] A.B. Olshen, E.S. Venkatraman (aka Venkatraman E. Seshan), R. Lucito and M. Wigler, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, 2004.
[2] E.S. Venkatraman and A.B. Olshen, A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 2007.

Examples

isEnvVarTRUE <- function(name) {
  value <- toupper(Sys.getenv(name))
  if (value == "yes") value <- "TRUE"
  isTRUE(as.logical(value))
}

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Number of loci
J <- 500

mu <- double(J)
mu[100:150] <- mu[100:150] + 1
mu[320:400] <- mu[320:400] - 1
eps <- rnorm(J, sd=1/2)
y <- mu + eps
x <- sort(runif(length(y), max=length(y))) * 1e5
w <- runif(J)
w[320:400] <- 0.001


cn <- RawCopyNumbers(y, x)
print(cn)

plot(cn, ylim=c(-3,3), col="#aaaaaa", xlab="Position (Mb)")

cnS <- binnedSmoothing(cn, by=500e3)
print(cnS)
lines(cnS, col="black", lwd=3)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Segment
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
legend <- c()

if (require("DNAcopy")) {
  fit <- segmentByCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="red", lwd=3)
  legend <- c(legend, red="CBS")
}

if (require("GLAD") && packageVersion("GLAD") != "9.9.9" &&
    !isEnvVarTRUE("_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_")) {
  fit <- segmentByGLAD(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="blue", lwd=3)
  legend <- c(legend, blue="GLAD")
}

if (require("HaarSeg")) {
  fit <- segmentByHaarSeg(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="orange", lwd=3)
  legend <- c(legend, orange="HaarSeg")
}

if (require("mpcbs")) {
  fit <- segmentByMPCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="white", lwd=6)
  drawLevels(cnr, col="purple", lwd=3)
  legend <- c(legend, purple="MPCBS")
}


if (length(legend) > 0) {
  legend("topleft", pch=19, col=names(legend), legend, bty="n", horiz=TRUE)
}

Segment copy numbers using the GLAD method

Description

Segment copy numbers using the GLAD method of the GLAD package.

Usage

## S3 method for class 'RawGenomicSignals'
segmentByGLAD(this, ..., flavor=c("glad", "daglad"), cache=FALSE, force=FALSE,
  verbose=FALSE)

Arguments

...

Additional arguments passed to the segmentation function.

flavor

A character string specifying what flavor of GLAD should be used.

verbose

See Verbose.

Details

Internally glad or daglad is used to segment the signals. This segmentation method does not support weighted segmentation.

Value

Returns the fit object.

Author(s)

Henrik Bengtsson

Segment copy numbers using the HaarSeg method

Description

Segment copy numbers using the HaarSeg method of the HaarSeg package.

Usage

## S3 method for class 'RawGenomicSignals'
segmentByHaarSeg(this, ..., cache=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to the segmentation function.

verbose

See Verbose.

Details

Internally haarSeg() of the HaarSeg is used to segment the signals. This segmentation method support weighted segmentation.

Value

Returns the fit object.

Author(s)

Henrik Bengtsson

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

Description

Segment copy numbers using the multi-platform CBS (mpCBS) method of the mpcbs package.

WARNING: The mpcbs package is an old package that is no longer maintained. It also has '_R_CHECK_LENGTH_1_CONDITION_' and '_R_CHECK_LENGTH_1_LOGIC2_' bugs, which give errors in R (>= 4.2.0). This means that 'segmentByMPCBS()' does not work in R (>= 4.2.0).

Usage

## S3 method for class 'RawGenomicSignals'
segmentByMPCBS(this, ..., cache=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to the segmentation function.

verbose

See Verbose.

Details

Internally mpcbs.mbic() of the mpcbs package is used for segmenting the signals. This segmentation method does not support weighted segmentation.

Value

Returns the fit object.

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data from multiple platforms
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Piecewise-constant copy-number state function
cnState <- function(x, ...) {
  n <- length(x)
  mu <- double(n)
  mu[20e6 <= x & x <= 30e6] <- +1
  mu[65e6 <= x & x <= 80e6] <- -1
  mu
} # cnState()

xMax <- 100e6

Js <- c(200, 400, 100)
bs <- c(1, 1.4, 0.5)
as <- c(0, +0.5, -0.5)
sds <- c(0.5, 0.3, 0.8)

cnList <- list()
for (kk in seq_along(Js)) {
  J <- Js[kk]
  a <- as[kk]
  b <- bs[kk]
  sd <- sds[kk]
  x <- sort(runif(J, max=xMax))
  mu <- a + b * cnState(x)
  eps <- rnorm(J, sd=sd)
  y <- mu + eps
  cn <- RawCopyNumbers(y, x)
  cnList[[kk]] <- cn
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Merge platform data (record their sources in 'id')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cn <- Reduce(append, cnList)
plot(cn, ylim=c(-3,3), col=cn$id)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Segment
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
legend <- c()

if (require("DNAcopy")) {
  fit <- segmentByCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="white", lwd=6)
  drawLevels(cnr, col="red", lwd=3)
  legend <- c(legend, red="CBS")
}


## WORKAROUND: There's a _R_CHECK_LENGTH_1_LOGIC2_ bug in
## mpcbs::mpcbs.mbic().  Until fixed, if ever, we cannot
## call segmentByMPCBS() here. /HB 2022-11-10
if (isTRUE(Sys.getenv("R_CHECK_FULL")) && require("mpcbs")) {
  fit <- segmentByMPCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="white", lwd=6)
  drawLevels(cnr, col="blue", lwd=3)
  legend <- c(legend, blue="MPCBS")
}


if (length(legend) > 0) {
  legend("topleft", pch=19, col=names(legend), legend, bty="n", horiz=TRUE)
}

Sets the alias of the output set

Description

Sets the alias of the output set. If specified, the alias overrides the data set name, which is used by default.

Usage

## S3 method for class 'Explorer'
setAlias(this, alias=NULL, ...)

Arguments

alias

A character string for the new alias of the output set. The alias must consists of valid filename characters, and must not contain commas, which are used to separate tags.

...

Not used.

Value

Returns itself invisibly.

Author(s)

Henrik Bengtsson

Sets the arrays

Description

Sets the arrays to be processed by the explorer.

Usage

## S3 method for class 'ChromosomeExplorer'
setArrays(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Sets the arrays

Description

Sets the arrays to be processed by the explorer.

Usage

## S3 method for class 'Explorer'
setArrays(...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Updates the Javascript file

Description

Updates the Javascript file.

Usage

## S3 method for class 'ChromosomeExplorer'
updateSetupExplorerFile(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns (invisibly) the pathname to the samples.js file.

Author(s)

Henrik Bengtsson

Writes the data file as a tab-delimited text file

Description

Writes the data file as a tab-delimited text file with or without file header comments.

Usage

## S3 method for class 'AromaUnitSignalBinaryFile'
writeDataFrame(this, filename=sprintf("%s.txt", getFilename(this)),
  path=file.path(getRootName(this, tags = "*,txt"), getParentName(this),
  getChipType(this, fullname = FALSE)), ..., columns=c("unitName", "*"), sep="\t",
  addHeader=TRUE, createdBy=NULL, nbrOfDecimals=4L,
  columnNamesPrefix=c("fullname", "name", "none"), overwrite=FALSE, verbose=FALSE)

Arguments

filename

The filename of the generated file.

path

The path where the generated file should be written.

...

Not used.

columns

A character vector specifying which column names, including optional annotation data column names, that should be exported. A string "*" corresponds to inserting the column names of the source data file.

sep

A character string specifying the column separator

addHeader

If TRUE, file header comments will be added that contain additional information about the source file and more.

createdBy

A character string specifying the createdBy file header comment. If NULL, the package version will be written.

nbrOfDecimals

An integer specifying the number of decimals for floating point columns.

columnNamesPrefix

A character string specifying what type of prefix should be used for column names.

overwrite

If TRUE, an existing destination file will be overwritten, otherwise an exception will be thrown.

verbose

A logical or a Verbose object.

Value

Returns the write data file as a TabularTextFile object.

Author(s)

Henrik Bengtsson

Writes the data set as a tab-delimited text file

Description

Writes the data set as a tab-delimited text file with or without file header comments.

We do neither recommend nor encourage the usage of this method - it is only available due to popular demand. For more details, see below.

Usage

## S3 method for class 'AromaUnitSignalBinarySet'
writeDataFrame(this, filename=sprintf("%s.txt", getFullName(this)),
  path=file.path(getRootName(this, tags = "*,txt"), getFullName(this), getChipType(this,
  fullname = FALSE)), ..., units=NULL, columns=c("unitName", "*"), sep="\t",
  addHeader=TRUE, createdBy=NULL, nbrOfDecimals=4L, ram=1,
  columnNamesPrefix=c("fullnames", "names", "none"), overwrite=FALSE, verbose=FALSE)

Arguments

filename

The filename of the generated file.

path

The path where the generated file should be written.

...

Not used.

units

The units to be written. If NULL, all units are considered.

columns

columnNamesPrefix

A character string specifying what type of prefix should be used for column names.

verbose

A logical or a Verbose object.

Value

Returns the written data set as a TabularTextFileSet object.

Warning

There is no limitation in how big the generated file can be. The bigger the data set is, the greater the file size will be. Because of this, we do neither recommend nor encourage the usage of this method. It is available only due to popular demand. Instead we recommend to write each file to a separate file. See writeDataFrame() of AromaUnitSignalBinaryFile for more information.

Author(s)

Henrik Bengtsson

Writes the data file as a tab-delimited text file

Description

Writes the data file as a tab-delimited text file with or without file header comments.

Usage

## S3 method for class 'AromaUnitTabularBinaryFile'
writeDataFrame(this, filename=sprintf("%s.txt", getFilename(this)),
  path=file.path(getRootName(this, tags = "*,txt"), getFullName(this), getChipType(this,
  fullname = FALSE)), ..., columns=c("unitName", "*"), sep="\t", addHeader=TRUE,
  createdBy=NULL, nbrOfDecimals=4L, columnNamesPrefix=c("fullname", "name", "none"),
  overwrite=FALSE, verbose=FALSE)

Arguments

filename

The filename of generated file.

path

The path where the generated file should be written.

...

Not used.

columns

sep

A character string specifying the column separator

addHeader

If TRUE, file header comments will be added that contain additional information about the source file and more.

createdBy

A character string specifying the createdBy file header comment. If NULL, the package version will be written.

nbrOfDecimals

An integer specifying the number of decimals for floating point columns.

columnNamesPrefix

A character string specifying what type of prefix should be used for column names.

overwrite

If TRUE, an existing destination file will be overwritten, otherwise an exception will be thrown.

verbose

A logical or a Verbose object.

Value

Returns the write data file as a TabularTextFile object.

Author(s)

Henrik Bengtsson

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

Description

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

Usage

## S3 method for class 'AromaTabularBinaryFile'
writeFooter(this, footer, ...)

Arguments

footer

A named list structure.

...

Not used.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Package aroma.core

Description

Installation and updates

License

Author(s)

References

The AbstractCNData class

Description

Usage

Arguments

Fields and Methods

Author(s)

The AbstractPSCNData class

Description

Usage

Arguments

Fields and Methods

Author(s)

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

Description

Usage

Arguments

Details

Author(s)

A binary file holding chromosome/position for each cell

Description

Usage

Arguments

Details

Author(s)

The AromaCellTabularBinaryFile class

Description

Usage

Arguments

Fields and Methods

Author(s)

See Also

The AromaGenomeTextFile class

Description

Usage

Arguments

Details

Fields and Methods

Author(s)

Examples

The abstract AromaMicroarrayDataFile class

Description

Usage

Arguments

Fields and Methods

Author(s)

See Also

The AromaMicroarrayDataSet class

Description

Usage

Arguments

Fields and Methods

Author(s)

The AromaMicroarrayDataSetTuple class

Description

Usage

Arguments

Fields and Methods

Author(s)

The AromaMicroarrayTabularBinaryFile class

Description

Usage

Arguments

Fields and Methods

Author(s)

See Also

The AromaPlatform class

Description

Usage

Arguments

Methods

Author(s)

Examples

The AromaPlatformInterface class

Description