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NEWS.md
In ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
Version 0.9.1 [2024-02-17]
Documentation
-
Add citation(package = "ACNE").
-
Fix minor Rd help-page issues.
Version 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.
Version 0.8.1 [2015-10-24]
Significant Changes
- ROBUSTNESS: Importing core R functions.
Version 0.8.0 [2015-02-23]
Bug Fixes
plot() for SnpNmfFit used undefined variable fit.
Miscellaneous
- ROBUSTNESS: Package test coverage is 49%.
Version 0.7.1 [2014-04-27]
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.
Version 0.7.0 [2013-10-17]
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).
Version 0.6.2 [2013-09-16]
Miscellaneous
- Bumped the package dependencies.
Version 0.6.1 [2013-08-23]
Significant Changes
- Now formally declaring S3 methods in NAMESPACE.
Version 0.6.0 [2013-08-21]
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.
Version 0.5.1 [2012-10-16]
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.
Version 0.5.0 [2011-10-24]
Significant Changes
- Added a NAMESPACE.
Version 0.4.3 [2011-08-01]
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).
Version 0.4.2 [2010-09-28]
New Features
- Improved validation of argument
refs.
Version 0.4.1 [2010-06-21]
New Features
- Added argument
refs to NmfPlm() and fitSnpNmf().
Miscellaneous
- Added more biocViews to the DESCRIPTION file.
Version 0.4.0 [2010-05-18]
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.
Version 0.3.0 [2010-05-17]
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).
Version 0.2.0 [2010-05-04]
Significant Changes
- Set the license to LGPL v2.1 or newer.
Miscellaneous
- Bumped up the version of the package dependencies.
Version 0.1.2 [2009-11-18]
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.
Version 0.1.1 [2009-11-11]
Miscellaneous
- Removed an obsolete
testScripts/.
Bug Fixes
- One of the
testScripts/ had a type.
Version 0.1.0 [2009-11-03]
Significant Changes
- Renamed package to ACNE (from aroma.affymetrix.nmf).
Miscellaneous
- Moved the package to the r-forge.r-project.org repository.
Version 0.0.5 [2009-03-25]
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().
Version 0.0.4 [2009-03-24]
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.
Version 0.0.3 [2009-02-02]
Miscellaneous
- Unknown changes.
Version 0.0.2 [2009-01-28]
Significant Changes
NmfPlm now inherits from ProbeLevelModel.
Deprecated and Defunct
-
Removed old MyProbeLevelModel class.
-
Created temporary package.
Version 0.0.1 [NA]
Significant Changes
- Created.
Try the ACNE package in your browser
Any scripts or data that you put into this service are public.
ACNE documentation built on May 29, 2024, 12:33 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Version 0.9.1 [2024-02-17]
Documentation
-
Add
citation(package = "ACNE"). -
Fix minor Rd help-page issues.
Version 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.
Version 0.8.1 [2015-10-24]
Significant Changes
- ROBUSTNESS: Importing core R functions.
Version 0.8.0 [2015-02-23]
Bug Fixes
plot()forSnpNmfFitused undefined variablefit.
Miscellaneous
- ROBUSTNESS: Package test coverage is 49%.
Version 0.7.1 [2014-04-27]
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.
Version 0.7.0 [2013-10-17]
Significant Changes
- Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE.
New Features
- Added argument
droptodoACNE()to be more consistent with similar methods in aroma.affymetrix, e.g.doRMA()anddoCRMAv2().
Documentation
-
Added a help page for
doACNE(). -
Added references to ACNE article.
Miscellaneous
-
CLEANUP: Removed all explicit calls to
gc()and replaced allrm()with fasterNULLassignments. -
Bumped the package dependencies.
-
Package now requires R (>= 2.15.0) and Bioconductor (>= 2.10.0).
Version 0.6.2 [2013-09-16]
Miscellaneous
- Bumped the package dependencies.
Version 0.6.1 [2013-08-23]
Significant Changes
- Now formally declaring S3 methods in NAMESPACE.
Version 0.6.0 [2013-08-21]
Significant Changes
- Now package no longer attaches ("loads") several of the dependent packages, e.g. R.methods, R.oo, matrixStats*, and MASS**.
Miscellaneous
-
Added
.Rbuildignoreto package so thatincl/and other directories/files are not included in the source build. -
Bumped the package dependencies.
Version 0.5.1 [2012-10-16]
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 '...' toNextMethod()- it'll do it for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version 0.5.0 [2011-10-24]
Significant Changes
- Added a NAMESPACE.
Version 0.4.3 [2011-08-01]
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).
Version 0.4.2 [2010-09-28]
New Features
- Improved validation of argument
refs.
Version 0.4.1 [2010-06-21]
New Features
- Added argument
refstoNmfPlm()andfitSnpNmf().
Miscellaneous
- Added more biocViews to the DESCRIPTION file.
Version 0.4.0 [2010-05-18]
Bug Fixes
- The
NmfSnpclass 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 inNmfPlm.
Version 0.3.0 [2010-05-17]
New Features
- Added
doACNE(). Added also redundancy tests for it.
Deprecated and Defunct
- Now a
flavortag is added toNmfPlm:s only ifflavor != "v4"(default).
Version 0.2.0 [2010-05-04]
Significant Changes
- Set the license to LGPL v2.1 or newer.
Miscellaneous
- Bumped up the version of the package dependencies.
Version 0.1.2 [2009-11-18]
Miscellaneous
- For debug purposes, the internal
NmfPlmfit function as well asfitSnpNmf()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]
Miscellaneous
- Removed an obsolete
testScripts/.
Bug Fixes
- One of the
testScripts/had a type.
Version 0.1.0 [2009-11-03]
Significant Changes
- Renamed package to ACNE (from aroma.affymetrix.nmf).
Miscellaneous
- Moved the package to the r-forge.r-project.org repository.
Version 0.0.5 [2009-03-25]
New Features
-
Added
fitSnpNmfArray(), which takes an Kx2xI array.fitSnpNmfArray()returns a list object of classSnpNmfFitfor which there is aplot()function. Note,fitSnpNmf()takes a 2KxI matrix. -
Added
snpMatrixToArray()andsnpArrayToMatrix().
Documentation
- Added example code with example data for
fitSnpNmfArray().
Version 0.0.4 [2009-03-24]
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.
Version 0.0.3 [2009-02-02]
Miscellaneous
- Unknown changes.
Version 0.0.2 [2009-01-28]
Significant Changes
NmfPlmnow inherits fromProbeLevelModel.
Deprecated and Defunct
-
Removed old
MyProbeLevelModelclass. -
Created temporary package.
Version 0.0.1 [NA]
Significant Changes
- Created.
Try the ACNE package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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