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drawC1C2Density() gained argument grid.Deprecated nbrOfFiles() methods; please use length() on corresponding input data sets.
Removed defunct callPeaks() for data.frame:s.
CLEANUP: Now doSegmentByPairedPSCBS() uses future_mapply() of future.apply instead of deprecated dsApplyInPairs() 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.
makeSmoothSplinePredict() defunct since Aug 2013. Made callPeaks() 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.
process() for AbstractCurveNormalization would generate an error due to read-only permissions introduced by copying the target file without resetting the file permissions.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.
doSegmentByPairedPSCBS() for AromaUnitPscnBinarySet.Updated package dependencies.
Package requires R (>= 2.15.1) and Bioconductor (>= 2.11.0).
points() for C1C2 passes (modified) argument x to NextMethod() as object = x.::: in calls.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().
**aroma.cn** Package object is also available when the package is only loaded (but not attached).CLEANUP: Now importing only what is needed from PSCBS.
Updated package dependencies.
byPath(), byName(), and findByPath() for PairedPSCBSFileSet was 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() for PairedPscbsModel would throw an error on getInputDataSet() not defined.
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.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.
PairedPSCBS to recognize when other mean-level estimators than the sample mean have been used.process() for PairedPscbsCaller used the global verbose.example() scripts used non-defined values.Now applicable classes utilize the new ParametersInterface.
DOCUMENTATION: Hiding more internal methods from the help indices.
cache: field modified instead of cached:. After correction, all clearCache() methods could be dropped.seq_along(x) instead of seq(along = x) everywhere. Similarly, seq(ds) where ds is GenericDataFileSet is now replaced by seq_along(ds). Likewise, seq_len(x) replaces seq(length = x), and length(ds) replaces nbrOfFiles(ds).whichVector() with which(), because the latter is now the fastest again.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 but R CMD check cannot known that.Arguments$get{Read,Writ}ablePath() instead of filePath(..., expandLinks = "any").Arguments$getWritablePath() everywhere instead of mkdirs(), 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.Object methods that calls “next” methods, utilizes NextMethod(), which became possible with R.oo v1.10.0.... 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.getOutputFileClass() and getOutputFileExtension() for TotalCnSmoothing.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 to segmentByPairedPSCBS().
PairedPscbsCaller.callPeaks(..., flavor="all") for PeaksAndValleys would return an error.calculateTumorPSCNByGenotype().fit() for PairedPscbsModel generates pair names iff tumor and normal names don’t match, e.g. GSM517071_vs_GSM517072 (if match then just Patient1). It also generated pair tags.DOCUMENTATION: Improved help on TotalCnBinnedSmoothing.
Bumped up the package dependencies.
PairedPscbsModel.Adopted findAtomicAberrations() for CBS from ditto of PairedPSCBS.
GENERALIZATION: Now plotTracks() for PruneCNA supports CBS segmentation results in additional to PairedPSCBS ones.
GENERALIZATION: Now pruneCNA() is implemented for AbstractCBS, not just PairedPSCBS objects.
Merged updates for findAtomicAberrations() for PairedPSCBS and some additional internal “equality” test functions.
normalizePrincipalCurve().drawC1C2Density() for PairedPSCBS would throw an exception if there was only one segment, or less than two finite (C1,C2):s.Updated package dependencies.
Additional internal updates.
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() of TotalCnSmoothing writes atomically.
Additional internal updates.
Updated package dependencies.
Additional internal updates.
Updated the package dependencies.
Some internal updates.
callPeaks() for PeaksAndValleys.Now deShearC1C2(), translateC1C2(), and transformC1C2() also update C1 and C2 mean levels.
Now using getLocusData() and getSegments() internally for all PairedPSCBS objects wherever applicable.
cat() and getOption() 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.
hpaste() internally wherever applicable.PairedPSCBSFile and PairedPSCBSFileSet.R CMD check.ROBUSTNESS: Now all bootstrap methods utilize resample().
Added more internal utility functions for future usage.
preserveScale to TumorBoostNormalization for 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 as XX from chr X.Package submitted to CRAN.
Updated citation information.
Package now requires aroma.core v1.6.0.
Package pass R CMD check on R v2.11.0 and v2.12.0 devel.
normalizeDifferencesToAverage(), normalizeTumorBoost(), callNaiveGenotypes(), and internal findPeaksAndValleys() to aroma.light v1.5.3.normalizeTumorBoost() could introduce NaN:s if betaN was 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() to MultiSourceCopyNumberNormalization.
h(.) and g(.) to AbstractCurveNormalization, which allows us to fit say on the log scale, e.g. h(x) = log2(x), g(y) = 2^y.getOutputDataSet() of AbstractCurveNormalization returned all files, not just the ones matching the input set.ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.
ROBUSTNESS: Now all index arguments are validated correctly using the new max argument of Arguments$getIndices(). Before the case where "max == 0" was not handled correctly.
flavor = "v4" of TumorBoostNormalization the default, and if used then no "flavor" tag is added.Now callXXorXY() and callNaiveGenotypes() 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 of callNaiveGenotypes().
Added Rd help to findPeaksAndValleys().
Now argument tol of findPeaksAndValleys() 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 check on R v2.10.0.
Added normalizeTumorBoost() for RawAlleleBFractions.
Added callGenotypes() for RawAlleleBFractions.
Added RawGenotypeCalls.
byPath() instead fromFiles().Renamed argument alignByChromosome for the constructor of the MultiSourceCopyNumberNormalization class to align in order to allow for more types of aligned.
The alignment of MultiSourceCopyNumberNormalization is now done using normalizeDifferencesToAverage(), which is robust against outliers, waviness, etc. The previous method which normalized toward the same overall median is no longer available.
normalizeDifferencesToAverage().getTags() of MultiSourceCopyNumberNormalization would return all asterisk tags as merged, e.g. c("mscn,align", "tagA", "tagB").XYCurveNormalization and PrincipalCurveNormalization.TumorBoostNormalization: the srcFiles attribute in file footer of the result files contained a duplicated default footer instead of the tumor-normal pair.callNaiveGenotype() and normalizeTumorBoost().Added model flavor "v4" which corrects heterozygots according to "v2" and homozygotes according to "v1".
Added new model flavor ("v3") of TumorBoostNormalization that is an extension of last weeks model flavor.
"v2") of TumorBoostNormalization that avoids over correcting (especially at the heterozygotes), but adjusting the correction factor. Use argument flavor = "v2".TumorBoostNormalization now only takes an AromaUnitGenotypeCallSet for argument gcN. It no longer takes an AromaUnitFracBCnBinarySet object, which was only an ad hoc solution.Added argument alignByChromosomes to MultiSourceCopyNumberNormalization. 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() to MultiSourceCopyNumberNormalization.
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 MultiSourceCopyNumberNormalization first 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() of MultiSourceCopyNumberNormalization only returns output data files with a matching fullname in the input set.
Added missing argument verbose in getTargetPositions() of TotalCnSmoothing. This caused unwanted verbose output in some cases.
process() of TotalCnSmoothing would not “recognize” fullname translators, that is, the output filenames were always identical to the input ones.
R CMD check and all redundancy tests.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.
backtransformPrincipalCurve().MultiSourceCopyNumberNormalization.R CMD check on R v2.7.1 and v2.8.0.extractRawCopyNumbers() of AromaTotalCnBinaryFile adds annotation data fields to the returned object, e.g. platform, chipType, and the fullname of the source file.normalizePrincipalCurve() and fitPrincipalCurve().ALPHA: Added extractRawCopyNumbers() to AromaTotalCnBinaryFile.
ALPHA: Added TotalCnSmoothing.
Aroma{Total|FreqB}CnSignal{File|Set}. With the more generalized aroma.core package, it is now possible retrieve the AromaUgpFile for the above. This provides the necessary basic methods for plotting data along chromosomes.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.