Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

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


Package: ACNE

Version: 0.8.0-9000 [2015-10-24] o ROBUSTNESS: Importing core R functions.

Version: 0.8.0 [2015-02-23] o ROBUSTNESS: Package test coverage is 49%. o BUG FIX: plot() for SnpNmfFit used undefined variable 'fit'.

Version: 0.7.1 [2014-04-27] o DOCUMENTATION: Rebuilt help pages which drop references to a few deprecated/private methods. o DOCUMENTATION: Clarified the example(fitSnpNmfArray). o ROBUSTNESS: Added package system tests. o Bumped package dependencies.

Version: 0.7.0 [2013-10-17] o Added argument 'drop' to doACNE() to be more consistent with similar methods in aroma.affymetrix, e.g. doRMA() and doCRMAv2(). o CLEANUP: Removed all explicit calls to gc() and replaced all rm() with faster NULL assignments. o DOCUMENTATION: Added a help page for doACNE(). o DOCUMENTATION: Added references to ACNE article. o ROBUSTNESS: Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE. o Bumped the package dependencies. o Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].

Version: 0.6.2 [2013-09-16] o Bumped the package dependencies.

Version: 0.6.1 [2013-08-23] o Now formally declaring S3 methods in NAMESPACE.

Version: 0.6.0 [2013-08-21] o CLEANUP: Now package no longer attaches ("loads") several of the dependent packages, e.g. R.methods, R.oo, matrixStats, MASS. o CLEANUP: Added .Rbuildignore to package so that incl/ and other directories/files are not included in the source build. o Bumped the package dependencies.

Version: 0.5.1 [2012-10-16] o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf. R-devel thread 'Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?' on Oct 16, 2012. o Now package imports utils, R.methodsS3 and R.oo.

Version: 0.5.0 [2011-10-24] o Added a NAMESPACE.

Version: 0.4.3 [2011-08-01] o WORKAROUND: In order for the package to work with the most recent version of R devel, which automatically add namespaces to packages who do not have one, we explicitly have specify that this package should use, for instance, cat() of R.utils (instead of 'base').

Version: 0.4.2 [2010-09-28] o ROBUSTIFICATION: Improved validation of argument 'refs'.

Version: 0.4.1 [2010-06-21] o Added more biocViews to the DESCRIPTION file. o Added argument 'refs' to NmfPlm() and fitSnpNmf().

Version: 0.4.0 [2010-05-18] o BUG FIX: The NmfSnp class would use a way too large threshold for deciding when the NMF algorithm has converged. The default accuracy 0.02 was replaced with 10.0 due to a "stray" argument in an internal function call. This bug has been there since March 24, 2009. o CLEAN UP: All flavors of NMF algorithms but the default one ("v4") is deprecated and no longer available in NmfPlm.

Version: 0.3.0 [2010-05-17] o Added doACNE(). Added also redundancy tests for it. o CLEAN UP: Now a flavor tag is added to NmfPlm:s only if flavor != "v4" (default).

Version: 0.2.0 [2010-05-04] o Bumped up the version of the package dependencies. o Set the license to LGPL v2.1 or newer.

Version: 0.1.2 [2009-11-18] o SPEED UP/CLEAN UP: For debug purposes, the internal NmfPlm fit function as well as fitSnpNmf() used to save the input data for each SNP fitted. This is now removed, and should speed up the processing substantially.

Version: 0.1.1 [2009-11-11] o BUG FIX: One of the testScripts/ had a type. o CLEAN UP: Removed an obsolete testScripts/.

Version: 0.1.0 [2009-11-03] o Moved the package to the repository. o Renamed package to ACNE (from aroma.affymetrix.nmf)

Version: 0.0.5 [2009-03-25] o Added example code with example data for fitSnpNmfArray(). o Added fitSnpNmfArray(), which takes an Kx2xI array. fitSnpNmfArray() returns a list object of class SnpNmfFit for which there is a plot() function. Note, fitSnpNmf() takes a 2KxI matrix. o Added snpMatrixToArray() and snpArrayToMatrix().

Version: 0.0.4 [2009-03-24] o Added sanity checks of all input and output to functions. o Added Rdoc comments (Rd help pages). o Removed obsolete dependency on the 'impute' package. o Cleaned up code.

Version: 0.0.3 [2009-02-02]

Version: 0.0.2 [2009-01-28] o CLEAN UP: Removed old MyProbeLevelModel class. o NmfPlm now inherits from ProbeLevelModel. o Created temporary package.

Version: 0.0.1 [2008-xx-xx] o Created.

Reference manual

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0.8.1 by Henrik Bengtsson, 6 years ago

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Browse source code at

Authors: Maria Ortiz [aut] , Henrik Bengtsson [aut, cre, cph] , Angel Rubio [aut]

Documentation:   PDF Manual  

LGPL (>= 2.1) license

Imports MASS, R.methodsS3, R.oo, R.utils, matrixStats, R.filesets, aroma.core

Depends on aroma.affymetrix

Suggests DNAcopy

See at CRAN