Package 'ACNE'

Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Authors: Maria Ortiz [aut], Henrik Bengtsson [aut, cre, cph], Angel Rubio [aut]
Maintainer: Henrik Bengtsson <[email protected]>
License: LGPL (>= 2.1)
Version: 0.9.1
Built: 2024-10-14 04:17:01 UTC
Source: https://github.com/HenrikBengtsson/ACNE

Help Index

Package ACNE

Description

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Installation and updates

This package requires the aroma.affymetrix package. To install this package, do: install.packages("ACNE")

To get started

  1. For a one-command pipeline, see the doACNE() method.

  2. For other usages, see the NmfPlm class.

License

LGPL (>= 2.1)

Author(s)

Maria Ortiz, Henrik Bengtsson, Angel Rubio

References

[1] M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010 [PMC2913655].

(ACNE)

Description

(ACNE) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

Usage

## S3 method for class 'AffymetrixCelSet'
doACNE(csR, fln=FALSE, drop=TRUE, verbose=FALSE, ...)
  ## Default S3 method:
doACNE(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).
fln

If TRUE, CRMAv2-style PCR fragment-length normalization is performed, otherwise not.
drop

If TRUE, the RMA summaries are returned, otherwise a named list of all intermediate and final results.
verbose

See Verbose.
...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise a named list of AromaUnitTotalCnBinarySet and AromaUnitFracBCnBinarySet.

Author(s)

Henrik Bengtsson

References

[1] M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010 [PMC2913655].

The NmfPlm class

Description

Package: ACNE
Class NmfPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NmfPlm

Directly known subclasses:
NmfSnpPlm

public abstract static class NmfPlm
extends ProbeLevelModel

This class represents the NMF model of [REF].

Usage

NmfPlm(..., maxIter=10L, maxIterRlm=20L, refs=NULL, flavor=c("v4", "v3", "v2", "v1"))

Arguments

...

Arguments passed to ProbeLevelModel.
maxIter

The maximum number of iteration in the NMF step.
maxIterRlm

A positive integer specifying the maximum number of iterations used in rlm.
refs

An index vector (integer or logical) specifying the reference samples. If NULL, all samples are used as a reference.
flavor

(Internal/developmental only) A character string specifying which algorithm to use.

Fields and Methods

Methods:

getAsteriskTags -

Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

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

References

[1] M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010 [PMC2913655].

See Also

Internally, for each SNP the NMF model is fitted using the fitSnpNmf() function.

The NmfSnpPlm class

Description

Package: ACNE
Class NmfSnpPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NmfPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NmfSnpPlm

Directly known subclasses:

public abstract static class NmfSnpPlm
extends SnpPlm

Usage

NmfSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to NmfPlm.
mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from NmfPlm:
getAsteriskTags

Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

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