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.