Add citation(package = "ACNE")
.
Fix minor Rd help-page issues.
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.
plot()
for SnpNmfFit
used undefined variable fit
.Rebuilt help pages which drop references to a few deprecated/private methods.
Clarified the example(fitSnpNmfArray)
.
Added package system tests.
Bumped package dependencies.
drop
to doACNE()
to be more consistent with similar methods in aroma.affymetrix, e.g. doRMA()
and doCRMAv2()
.Added a help page for doACNE()
.
Added references to ACNE article.
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).
Added .Rbuildignore
to package so that incl/
and other directories/files are not included in the source build.
Bumped the package dependencies.
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.cat()
of R.utils (instead of base).refs
.refs
to NmfPlm()
and fitSnpNmf()
.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."v4"
) is deprecated and no longer available in NmfPlm
.doACNE()
. Added also redundancy tests for it.flavor
tag is added to NmfPlm
:s only if flavor != "v4"
(default).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.testScripts/
.testScripts/
had a type.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()
.
fitSnpNmfArray()
.Added sanity checks of all input and output to functions.
Cleaned up code.
NmfPlm
now inherits from ProbeLevelModel
.Removed old MyProbeLevelModel
class.
Created temporary package.