- ...
- Fix minor help-page issues.
drawC1C2Density()gained argumentgrid.
-
Deprecated
nbrOfFiles()methods; please uselength()on corresponding input data sets. -
Removed defunct
callPeaks()for data.frame:s.
-
CLEANUP: Now
doSegmentByPairedPSCBS()usesfuture_mapply()of future.apply instead of deprecateddsApplyInPairs()of R.filesets. -
Utilizing subsetted calculations of matrixStats (>= 0.50.0).
-
CLEANUP: Now importing generic
extractC1C2()from PSCBS to avoid creating a new one.
-
Package now requires R (>= 3.1.1) released July 2014. This allows us to use Bioconductor (>= 3.0) (October 2014).
-
Bumped package dependencies.
-
ROBUSTNESS: Explicitly importing core R functions.
- Removed
makeSmoothSplinePredict()defunct since Aug 2013. MadecallPeaks()for data.frame:s defunct (was deprecated).
-
ROBUSTNESS: Added the first package tests.
-
Bumped package dependencies.
-
Package now requires R (>= 3.0.3) and Bioconductor (>= 2.13) which were released March 2014 and are in fact old; it's recommended to use a more recent version of R.
- ROBUSTNESS: Package now does a better job importing objects from suggested packages.
- It could be that
process()forAbstractCurveNormalizationwould generate an error due to read-only permissions introduced by copying the target file without resetting the file permissions.
- Added a few missing NAMESPACE imports.
-
Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were released April 2013 and are in fact old and it's recommended to use a more recent version of R.
-
Updated package dependencies.
- Added
doSegmentByPairedPSCBS()forAromaUnitPscnBinarySet.
-
Updated package dependencies.
-
Package requires R (>= 2.15.1) and Bioconductor (>= 2.11.0).
- ROBUSTNESS: Now
points()forC1C2passes (modified) argumentxtoNextMethod()asobject = x.
- Updated package dependencies.
- CLEANUP: Package no longer uses
:::in calls.
- CLEANUP: Removed several internal prototype methods no longer needed or that have been moved to the (private) Mikado package.
-
Minor tweaks to NAMESPACE.
-
Updated package dependencies.
-
Package requires R (>= 2.15.0) and Bioconductor (>= 2.10.0).
-
ROBUSTNESS: Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE.
-
CLEANUP: Dropped obsolete usage of
autoload().
- Now the
**aroma.cn**Package object is also available when the package is only loaded (but not attached).
- Updated package dependencies.
- Forgot to import several functions from matrixStats. These went undetected because aroma.light (< 1.31.6) attached the matrixStats in the past.
-
CLEANUP: Now importing only what is needed from PSCBS.
-
Updated package dependencies.
- More internal updates.
-
byPath(),byName(), andfindByPath()forPairedPSCBSFileSetwas also affected by the bug described in the 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. -
getPath()forPairedPscbsModelwould throw an error ongetInputDataSet()not defined.
- Made
makeSmoothSplinePredict()defunct.
-
SPEEDUP: Replaced all
rm()calls with NULL assignments. Also removed several explicit garbage collector calls. -
CLEANUP: The formal package dependency on Bioconductor package aroma.light has been relaxed so the package can be installed without it.
-
CLEANUP: Package now only imports R.oo.
-
Updated package dependencies.
-
CRAN POLICY: Now all Rd
\usage{}lines are at most 90 characters long. -
CRAN POLICY: Now all Rd example lines are at most 100 characters long.
findNeutralCopyNumberState()is now in PSCBS.
- Utilizing new
startupMessage()of R.oo.
-
Updated package dependencies.
-
CLEANUP: No longer using deprecated PSCBS methods.
-
ROBUSTNESS:
{load,save}Cache()from R.cache are now explicitly imported in the namespace.
- Updated internal methods for
PairedPSCBSto recognize when other mean-level estimators than the sample mean have been used.
process()forPairedPscbsCallerused the globalverbose.
- Bumped up the package dependencies.
- Some
example()scripts used non-defined values.
- Bumped up the package dependencies.
-
Now applicable classes utilize the new
ParametersInterface. -
DOCUMENTATION: Hiding more internal methods from the help indices.
- CLEANUP/FIX: Used
cache:field modified instead ofcached:. After correction, allclearCache()methods could be dropped.
- CLEANUP: Now
seq_along(x)instead ofseq(along = x)everywhere. Similarly,seq(ds)wheredsisGenericDataFileSetis now replaced byseq_along(ds). Likewise,seq_len(x)replacesseq(length = x), andlength(ds)replacesnbrOfFiles(ds).
- CLEANUP: Replaced all
whichVector()withwhich(), because the latter is now the fastest again.
- ROBUSTNESS: Now package also imports PSCBS to please
R CMD check. The reason was that some of the internal methods call PSCBS methods, which only happens if PSCBS is loaded in the first place butR CMD checkcannot known that.
- CLEANUP: Now using
Arguments$get{Read,Writ}ablePath()instead offilePath(..., expandLinks = "any").
- ROBUSTNESS: Now using
Arguments$getWritablePath()everywhere instead ofmkdirs(), because the former will do a better job in creating and asserting directories on slow shared file systems, and when it fails it gives a more informative error message.
- ROBUSTNESS: Now all static
Objectmethods that calls "next" methods, utilizesNextMethod(), which became possible with R.oo v1.10.0.
- ROBUSTNESS/BUG FIX: No longer passing
...toNextMethod(), 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.
- Added
getOutputFileClass()andgetOutputFileExtension()forTotalCnSmoothing.
- More internal updates.
-
Now
PairedPscbsCaller()passes...to the internal callers, which makes it possible to for instance specify the number of bootstrap samples done for the AB caller. -
Now
PairedPscbsModel()excludes the actual gaps from the known segments it passes tosegmentByPairedPSCBS().
- Added trial version of
PairedPscbsCaller.
callPeaks(..., flavor="all")forPeaksAndValleyswould return an error.
- Additional internal updates.
- Added
calculateTumorPSCNByGenotype().
- Now
fit()forPairedPscbsModelgenerates pair names iff tumor and normal names don't match, e.g.GSM517071_vs_GSM517072(if match then justPatient1). It also generatedpairtags.
- Bumped up the package dependencies.
- Bumped up the package dependencies.
-
DOCUMENTATION: Improved help on
TotalCnBinnedSmoothing. -
Bumped up the package dependencies.
- Added trial version of
PairedPscbsModel.
-
Adopted
findAtomicAberrations()forCBSfrom ditto ofPairedPSCBS. -
GENERALIZATION: Now
plotTracks()forPruneCNAsupportsCBSsegmentation results in additional toPairedPSCBSones. -
GENERALIZATION: Now
pruneCNA()is implemented forAbstractCBS, not justPairedPSCBSobjects. -
Merged updates for
findAtomicAberrations()forPairedPSCBSand some additional internal "equality" test functions.
- Updated package dependencies.
- Updated package dependencies.
- Updated package dependencies.
- Added help for
normalizePrincipalCurve().
- One of the PSCBS examples gave an error.
drawC1C2Density()forPairedPSCBSwould throw an exception if there was only one segment, or less than two finite (C1,C2):s.
- Moved some internal functions to the PSCBS package, so package dependencies was also updated.
-
Updated package dependencies.
-
Additional internal updates.
- Added
TotalCnBinnedSmoothing().
-
CLEANUP: The example code for the internal PairedPSCBS methods now only runs if environment variable
_R_CHECK_FULL_is set. This makes the package easier on the CRAN servers. -
ROBUSTNESS: Updated package dependencies.
-
ROBUSTNESS: Now
process()ofTotalCnSmoothingwrites atomically. -
Additional internal updates.
-
Updated package dependencies.
-
Additional internal updates.
-
Updated the package dependencies.
-
Some internal updates.
- Updated the memoiziation keys for some of the PairedPSCBS methods so that results prior to PSCBS v0.13.3 will not be retrieved.
- Added Rdoc comments to
callPeaks()forPeaksAndValleys.
- Added a namespace to the package, which will be more or less a requirement starting with R v2.14.0.
-
Now
deShearC1C2(),translateC1C2(), andtransformC1C2()also update C1 and C2 mean levels. -
Now using
getLocusData()andgetSegments()internally for allPairedPSCBSobjects wherever applicable.
- The aroma.cn v0.8.1 tarball uploaded to CRAN mistakenly contained a NAMESPACE file, which shouldn't have been there.
- 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
cat()andgetOption()of R.utils (instead of base).
-
Forgot to update some examples and test scripts which were still referring to the old psCBS package (should be PSCBS).
-
Updated internal code to work with the new column names in PSCBS v0.11.0.
- CLEANUP: Removed some internal functions from the help index.
- ROBUSTNESS: Updated package dependencies.
- Now package refers to PSCBS package (not old psCBS).
- CLEANUP: Utilizing
hpaste()internally wherever applicable.
- Fixed a small code typo that didn't make a difference.
- Added beta classes
PairedPSCBSFileandPairedPSCBSFileSet.
- Removed a NOTE from
R CMD check.
-
ROBUSTNESS: Now all bootstrap methods utilize
resample(). -
Added more internal utility functions for future usage.
- Added more internal utility functions for future usage.
- Added more internal utility functions for future usage.
- Added more internal utility functions for future usage.
- Added internal utility functions for future usage.
- Added option
preserveScaletoTumorBoostNormalizationfor correcting for signal compression in heterozygous SNPs. The defaults is to do this correction.
callXXorXY()no longer calls gender from chr Y, when gender is estimated asXXfrom chr X.
-
Package submitted to CRAN.
-
Updated citation information.
-
Package now requires aroma.core v1.6.0.
-
Package pass
R CMD checkon R v2.11.0 and v2.12.0 devel.
- Moved
normalizeDifferencesToAverage(),normalizeTumorBoost(),callNaiveGenotypes(), and internalfindPeaksAndValleys()to aroma.light v1.5.3.
- For flavors "v2" and "v3",
normalizeTumorBoost()could introduce NaN:s ifbetaNwas exactly zero or exactly one.
-
Added (for now internal) option to change the degrees of freedom of the fitted principal curves in MSCN.
-
Added
plotSmoothedPairsOne()toMultiSourceCopyNumberNormalization.
- Added support for transform/untransform functions
h(.)andg(.)toAbstractCurveNormalization, which allows us to fit say on the log scale, e.g.h(x) = log2(x),g(y) = 2^y.
getOutputDataSet()ofAbstractCurveNormalizationreturned all files, not just the ones matching the input set.
-
ROBUSTNESS: Using new
Arguments$getInstanceOf()were possible. -
ROBUSTNESS: Now all index arguments are validated correctly using the new
maxargument ofArguments$getIndices(). Before the case where"max == 0"was not handled correctly.
- Made
flavor = "v4"ofTumorBoostNormalizationthe default, and if used then no"flavor"tag is added.
-
Now
callXXorXY()andcallNaiveGenotypes()handles missing values and non-finite values. They also censor outliers to become infinite/extreme values. -
Added
callXXorXY(). -
Added an
example()to the Rd help ofcallNaiveGenotypes(). -
Added Rd help to
findPeaksAndValleys(). -
Now argument
toloffindPeaksAndValleys()can be zero; before it had to be at least the smallest possible double.
-
CLEANUP: Removed suggested dependency on princurve, which is now indirectly suggested/requested via aroma.light.
-
More recent dependencies on Bioconductor packages.
-
Package passes
R CMD checkon R v2.10.0.
-
Added
normalizeTumorBoost()forRawAlleleBFractions. -
Added
callGenotypes()forRawAlleleBFractions. -
Added
RawGenotypeCalls.
- CLEAN UP: Updated to use
byPath()insteadfromFiles().
-
Renamed argument
alignByChromosomefor the constructor of theMultiSourceCopyNumberNormalizationclass toalignin order to allow for more types of aligned. -
The alignment of
MultiSourceCopyNumberNormalizationis now done usingnormalizeDifferencesToAverage(), which is robust against outliers, waviness, etc. The previous method which normalized toward the same overall median is no longer available.
- Added
normalizeDifferencesToAverage().
getTags()ofMultiSourceCopyNumberNormalizationwould return all asterisk tags as merged, e.g.c("mscn,align", "tagA", "tagB").
- ADDED:
XYCurveNormalizationandPrincipalCurveNormalization.
TumorBoostNormalization: thesrcFilesattribute in file footer of the result files contained a duplicated default footer instead of the tumor-normal pair.
- Added low-level
callNaiveGenotype()andnormalizeTumorBoost().
-
Added model flavor
"v4"which corrects heterozygots according to"v2"and homozygotes according to"v1". -
Added new model flavor (
"v3") ofTumorBoostNormalizationthat is an extension of last weeks model flavor.
- Added an optional flavor (
"v2") ofTumorBoostNormalizationthat avoids over correcting (especially at the heterozygotes), but adjusting the correction factor. Use argumentflavor = "v2".
- The constructor of
TumorBoostNormalizationnow only takes anAromaUnitGenotypeCallSetfor argumentgcN. It no longer takes anAromaUnitFracBCnBinarySetobject, which was only an ad hoc solution.
-
Added argument
alignByChromosomestoMultiSourceCopyNumberNormalization. If TRUE, the signals are shifted per chromosome such that the mean of the normalized smoothed signals is the same for all sources. This can for instance remove systematic effects on sex chromosomes added by some ad hoc preprocessing methods. -
Added a
clearCache()toMultiSourceCopyNumberNormalization. -
ALPHA: Added
TumorBoostNormalization. -
INTERNAL: Added foundations for TumorBoost, i.e. in memory classes such as
TotalAndFracBSnpData. -
INTERNAL: Added
findPeaksAndValleys(). -
ROBUSTNESS: Now all constructors report on unknown arguments.
-
ROBUSTNESS: Now
MultiSourceCopyNumberNormalizationfirst write normalized data to a temporary file, which is then renamed. This lower the risk for having incomplete data in case of interrupts. -
Now
getOutputDataSets()ofMultiSourceCopyNumberNormalizationonly returns output data files with a matching fullname in the input set.
-
Added missing argument
verboseingetTargetPositions()ofTotalCnSmoothing. This caused unwanted verbose output in some cases. -
process()ofTotalCnSmoothingwould not "recognize" fullname translators, that is, the output filenames were always identical to the input ones.
- Package passes
R CMD checkand all redundancy tests.
- Minor update in order to work with new
RawGenomicSignals.
-
Added redundancy tests to package.
-
Further cleanup. Some functions are now in aroma.light.
-
{fit|backtransform}PrincipalCurve()were moved to aroma.light v1.11.1. -
Several classes and methods were moved to aroma.core v1.0.0.
-
Adopted the package to the new classes of aroma.core.
- ALPHA: Added
backtransformPrincipalCurve().
- Added alpha version of
MultiSourceCopyNumberNormalization.
- Fixed some broken cross links in the Rd help. Package pass
R CMD checkon R v2.7.1 and v2.8.0.
- Now
extractRawCopyNumbers()ofAromaTotalCnBinaryFileadds annotation data fields to the returned object, e.g. platform, chipType, and the fullname of the source file.
- ALPHA: Added
normalizePrincipalCurve()andfitPrincipalCurve().
-
ALPHA: Added
extractRawCopyNumbers()toAromaTotalCnBinaryFile. -
ALPHA: Added
TotalCnSmoothing.
- Package now provides platform-independent classes
Aroma{Total|FreqB}CnSignal{File|Set}. With the more generalized aroma.core package, it is now possible retrieve theAromaUgpFilefor the above. This provides the necessary basic methods for plotting data along chromosomes.
- Created.