NEWS

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ACNE 0.9.1 (2024-02-17)

Documentation

• Add citation(package = "ACNE").

• Fix minor Rd help-page issues.

ACNE 0.9.0 (2023-06-25)

Miscellaneous

• Made NMF initialization a bit faster by calling matrixStats functions with optimized subsetting of rows and columns.

• Importing throw() from R.oo instead of R.methodsS3.

ACNE 0.8.1 (2015-10-27)

Significant Changes

• ROBUSTNESS: Importing core R functions.

ACNE 0.8.0 (2015-02-23)

Bug Fixes

• plot() for SnpNmfFit used undefined variable fit.

Miscellaneous

• ROBUSTNESS: Package test coverage is 49%.

ACNE 0.7.1

Documentation

• Rebuilt help pages which drop references to a few deprecated/private methods.

• Clarified the example(fitSnpNmfArray).

Miscellaneous

• Added package system tests.

• Bumped package dependencies.

ACNE 0.7.0 (2013-10-19)

Significant Changes

• Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE.

New Features

• Added argument drop to doACNE() to be more consistent with similar methods in aroma.affymetrix, e.g. doRMA() and doCRMAv2().

Documentation

• Added a help page for doACNE().

• Added references to ACNE article.

Miscellaneous

• CLEANUP: Removed all explicit calls to gc() and replaced all rm() with faster NULL assignments.

• Bumped the package dependencies.

• Package now requires R (>= 2.15.0) and Bioconductor (>= 2.10.0).

ACNE 0.6.2

Miscellaneous

• Bumped the package dependencies.

ACNE 0.6.1

Significant Changes

• Now formally declaring S3 methods in NAMESPACE.

ACNE 0.6.0

Significant Changes

• Now package no longer attaches ("loads") several of the dependent packages, e.g. R.methods, R.oo, *matrixStats, and MASS.

Miscellaneous

• Added .Rbuildignore to package so that incl/ and other directories/files are not included in the source build.

• Bumped the package dependencies.

ACNE 0.5.1

Significant Changes

• Now package imports utils, R.methodsS3, and R.oo.

Bug Fixes

• 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.

ACNE 0.5.0 (2011-10-25)

Significant Changes

• Added a NAMESPACE.

ACNE 0.4.3 (2011-09-16)

Significant Changes

• 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).

ACNE 0.4.2

New Features

• Improved validation of argument refs.

ACNE 0.4.1

New Features

• Added argument refs to NmfPlm() and fitSnpNmf().

Miscellaneous

• Added more biocViews to the DESCRIPTION file.

ACNE 0.4.0

Bug Fixes

• 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.

Deprecated and Defunct

• All flavors of NMF algorithms but the default one ("v4") is deprecated and no longer available in NmfPlm.

ACNE 0.3.0

New Features

• Added doACNE(). Added also redundancy tests for it.

Deprecated and Defunct

• Now a flavor tag is added to NmfPlm:s only if flavor != "v4" (default).

ACNE 0.2.0

Significant Changes

• Set the license to LGPL v2.1 or newer.

Miscellaneous

• Bumped up the version of the package dependencies.

ACNE 0.1.2

Miscellaneous

• 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.

ACNE 0.1.1

Miscellaneous

• Removed an obsolete testScripts/.

Bug Fixes

• One of the testScripts/ had a type.

ACNE 0.1.0

Significant Changes

• Renamed package to ACNE (from aroma.affymetrix.nmf).

Miscellaneous

• Moved the package to the r-forge.r-project.org repository.

ACNE 0.0.5

New Features

• 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.

• Added snpMatrixToArray() and snpArrayToMatrix().

Documentation

• Added example code with example data for fitSnpNmfArray().

ACNE 0.0.4

Significant Changes

• Removed obsolete dependency on the impute package.

Documentation

• Added Rdoc comments (Rd help pages).

Miscellaneous

• Added sanity checks of all input and output to functions.

• Cleaned up code.

ACNE 0.0.3

Miscellaneous

• Unknown changes.

ACNE 0.0.2

Significant Changes

• NmfPlm now inherits from ProbeLevelModel.

Deprecated and Defunct

• Removed old MyProbeLevelModel class.

• Created temporary package.

ACNE 0.0.1

Significant Changes

• Created.