[med-svn] [r-cran-pscbs] 01/06: New upstream version 0.63.0
Andreas Tille
tille at debian.org
Tue Oct 24 14:43:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-pscbs.
commit 6e6d7e1b4c255685909bce2278a150dc11c91a37
Author: Andreas Tille <tille at debian.org>
Date: Tue Oct 24 16:25:29 2017 +0200
New upstream version 0.63.0
---
DESCRIPTION | 26 +-
INSTALL.md | 3 +-
NAMESPACE | 10 +-
NEWS | 3611 ++++++++++++++++++++++------------
R/CBS.CALL.R | 3 -
R/CBS.R | 2 +-
R/NonPairedPSCBS.R | 2 +-
R/PSCBS.isLocallyPhased.R | 12 +
R/PairedPSCBS.R | 4 +-
R/PairedPSCBS.callCopyNeutral.R | 69 +-
R/PairedPSCBS.estimateKappa.R | 3 -
R/callSegmentationOutliers.R | 4 -
R/findNeutralCopyNumberState.R | 4 -
R/segmentByCBS.R | 5 -
R/segmentByNonPairedPSCBS.R | 1 -
R/segmentByPairedPSCBS.R | 4 +-
R/zzz.R | 64 +-
README.md | 10 +-
appveyor.yml | 11 +-
cran-comments.md | 54 +-
incl/999.missingdocs.txt | 2 +
man/Non-documented_objects.Rd | 2 +
man/NonPairedPSCBS.Rd | 2 +-
man/PSCBS.Rd | 1 +
man/PairedPSCBS.Rd | 2 +-
man/estimateDeltaCN.PairedPSCBS.Rd | 6 +-
revdep/README.md | 89 +-
revdep/problems.md | 28 +-
revdep/timing.md | 22 +-
tests/segmentByCBS,futures.R | 10 +-
tests/segmentByPairedPSCBS,futures.R | 4 +-
31 files changed, 2592 insertions(+), 1478 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 1a1c6db..9f0df8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,31 +1,30 @@
Package: PSCBS
-Version: 0.62.0
+Version: 0.63.0
Depends:
- R (>= 3.1.2),
+ R (>= 3.2.0),
utils
Imports:
R.methodsS3 (>= 1.7.1),
R.oo (>= 1.21.0),
R.utils (>= 2.5.0),
R.cache (>= 0.12.0),
- matrixStats (>= 0.51.0),
- DNAcopy (>= 1.40.0),
+ matrixStats (>= 0.52.2),
+ aroma.light (>= 2.4.0),
+ DNAcopy (>= 1.42.0),
listenv (>= 0.6.0),
- future (>= 1.1.1),
+ future (>= 1.5.0),
parallel
Suggests:
Hmisc (>= 3.16-0),
- R.rsp (>= 0.30.0),
- R.devices (>= 2.15.0),
- ggplot2 (>= 1.0.1),
- aroma.light (>= 2.2.1)
+ R.rsp (>= 0.41.0),
+ R.devices (>= 2.15.1),
+ ggplot2 (>= 2.2.1)
SuggestsNote:
- BioC (>= 3.0),
+ BioC (>= 3.1),
Recommended:
- Hmisc,
- aroma.light
+ Hmisc
VignetteBuilder: R.rsp
-Date: 2016-11-10
+Date: 2017-06-27
Title: Analysis of Parent-Specific DNA Copy Numbers
Authors at R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
@@ -42,3 +41,4 @@ ByteCompile: TRUE
biocViews: aCGH, CopyNumberVariants, SNP, Microarray, OneChannel, TwoChannel, Genetics
URL: https://github.com/HenrikBengtsson/PSCBS
BugReports: https://github.com/HenrikBengtsson/PSCBS/issues
+RoxygenNote: 6.0.1
diff --git a/INSTALL.md b/INSTALL.md
index 06ab572..1c712c1 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -7,8 +7,7 @@ by adding the following
future::plan("multiprocess")
```
to the beginning of the PSCBS script. Everything else will work the
-same. To reset to non-parallel (synchronously) processing, use
-`future::plan("eager")`.
+same. To reset to non-parallel processing, use `future::plan("sequential")`.
To configure this automatically whenever the package is loaded, see
future vignette '[A Future for R: Controlling Default Future Strategy](https://cran.r-project.org/web/packages/future/vignettes/future-4-startup.html)'.
diff --git a/NAMESPACE b/NAMESPACE
index 6c6aa7d..79e4877 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -38,9 +38,6 @@ importFrom("matrixStats",
"binMeans", "colCumsums", "colDiffs", "colMins", "colMaxs",
"rowAlls", "rowAnys", "rowMins", "weightedMedian")
-importFrom("DNAcopy",
- "segments.summary", "smooth.CNA", "CNA", "segment", "getbdry")
-
importFrom("graphics",
"abline", "arrows", "axis", "box", "lines",
"mtext", "par", "plot", "points", "rect", "text")
@@ -57,6 +54,12 @@ importFrom("utils",
"head", "packageVersion", "str", "tail", "write.table",
"packageDescription")
+importFrom("aroma.light",
+ "callNaiveGenotypes", "findPeaksAndValleys", "normalizeTumorBoost")
+
+importFrom("DNAcopy",
+ "segments.summary", "smooth.CNA", "CNA", "segment", "getbdry")
+
importFrom("listenv", "listenv")
importFrom("future", "%<-%")
importFrom("parallel", "nextRNGStream")
@@ -357,5 +360,6 @@ S3method("getLocusData", "PSCBS")
S3method("getLocusSignalNames", "PSCBS")
S3method("getSegments", "PSCBS")
S3method("getSegmentTrackPrefixes", "PSCBS")
+S3method("isLocallyPhased", "PSCBS")
S3method("isSegmentSplitter", "PSCBS")
S3method("writeSegments", "PSCBS")
diff --git a/NEWS b/NEWS
index d820a7e..2fa869d 100644
--- a/NEWS
+++ b/NEWS
@@ -1,1768 +1,2889 @@
Package: PSCBS
==============
-Version: 0.62.0 [2016-11-10]
-o Added normalizeTotalCNs() for PSCBS objects.
-o REPORTS: Updated report template for PairedPSCBS object such
- that reports are also generated from DH-only data, i.e. when
- there are no BAF signals (which may happen with DNA-Seq data).
-o Added splitters=TRUE as the default for setSegments().
-o CLEANUP: Minor internal cleanup and restructuring.
+Version: 0.63.0 [2017-06-27]
+SIGNIFICANT CHANGES:
+ o Package now depends on R (>= 3.2.0) and Bioconductor (>= 3.1) packages.
-Version: 0.61.0 [2016-02-03]
-o Package now requires R (>= 3.1.2) released October 2014, because
- of its dependency on the listenv package.
-o segmentByPairedPSCBS() gained argument 'rho' for paired PSCBS
- segmentation on total CNs (TCNs) and decrease-of-heterozygosity
- signals (DHs) as an alternative to for instance TCN and
- allele B fractions (BAFs).
-o BUG FIX: Segmentation using futures where not fully reproducible
- when known segments where specified. Fixed by changing how the
- random number stream is set and used.
+NEW FEATURES:
+ o estimateDeltaCN() for PairedPSCBS gained argument 'flavor' and new estimator
+ `flavor = "delta(mode)".
-Version: 0.60.0 [2015-11-17]
-o PARALLEL: Add support for parallel processing via futures by
- utilizing the future package. Parallel segmentation over multiple
- chromosomes (or known segments) done by segmentByCBS() and
- segmentByPairedPSCBS() is enabled by future::plan("multicore").
-o REPRODUCIBILITY: Whenever argument 'seed' is given, the
- L'Ecuyer-CMRG stream is now used to generate random numbers.
- For backward compatibility with other types of random number
- generators, don't specify argument 'seed' but instead use
- set.seed() to set the seed before calling the method.
-o Bump package dependencies.
+ o Added isLocallyPhased() for PSCBS.
+CODE REFACTORING:
-Version: 0.50.0 [2015-10-14]
-o Now argument 'preserveScale' for segmentByPairedPSCBS() defaults
- to FALSE. In the past the default has effectively been TRUE, but
- has given a warning since v0.43.0 (June 2014) that it eventually
- will be changed to FALSE. Now it will give a warning that it
- has changed, unless the option is explicitly specified. This
- new warning will eventually be removed in a future version.
+ o Now package imports aroma.light instead of only suggesting it.
+ o Package tests no longer test against the deprecated lazy strategy of future.
-Version: 0.45.1 [2015-09-16]
-o More informative error messages when append() for CBS or PSCBS fail.
-o BUG FIX: segmentByCBS(, ..., w, knownSegments) would give internal
- assertion errors if one of the priorly known segments would have
- zero data points. Thanks to Kirill Tsukanov (Moscow) and
- Eric Talevich (UCSF) for reporting on this.
+Version: 0.62.0 [2016-11-10]
-Version: 0.45.0 [2015-09-11]
-o segmentByCBS() gained argument 'avg'.
-o Add writeWIG() for CBS objects.
-o pruneByHClust() no longer gives a message about method "ward"
- is now named "ward.D".
-o Added skip=TRUE to report().
-o ROBUSTNESS: Package test coverage is 62%.
-o ROBUSTNESS: Explicitly importing core R functions.
-o FIX: plotTracks() for CBS ignored arguments 'cex', 'col' and
- 'meanCol' if two or more chromosomes were plotted.
-o BUG FIX: joinSegments(), resetSegments() and pruneBySdUndo() gave
- errors for multi-chromosome (>= 2) segmentation results.
-o BUG FIX: segmentByCBS() would ignore argument 'w' (weights) if
- more than one chromosome was fitted.
-o BUG FIX: tileChromosomes() for CBS returned incorrect locus data.
-o BUG FIX: gapsToSegments(gaps) gave an error if nrow(gaps) == 0
- or contained no 'chromosome' column.
-o BUG FIX: findLargeGaps() could return NULL. Now it always returns
- a data.frame.
-o BUG FIX: The report() RSP-embedded TeX templates for CBS and
- PairedPSCBS data did not escape sample and data set names
- to LaTeX in all places needed.
-o Package now requires R (>= 3.1.1) released July 2014. This allows
- us to use BioC (>= 3.0) (October 2014).
+NEW FEATURES:
+ o Added normalizeTotalCNs() for PSCBS objects.
-Version: 0.44.0 [2015-02-22]
-o ROBUSTNESS: Package test coverage is 58%.
-o ROBUSTNESS: Forgot to declare some S3 methods in NAMESPACE.
-o SPEEDUP: Now using more functions of matrixStats.
-o CLEANUP: bootstrapDHByRegion() is defunct (was deprecated since 2013).
-o Package now requires R (>= 3.0.3) and BioC (>= 2.13), which are
- from March 2014 and are in fact old. It's recommended to use a
- more recent version of R.
+ o REPORTS: Updated report template for PairedPSCBS object such that reports
+ are also generated from DH-only data, i.e. when there are no BAF signals
+ (which may happen with DNA-Seq data).
+ o Added splitters = TRUE as the default for setSegments().
-Version: 0.43.0 [2014-06-08]
-o Now segmentByPairedPSCBS() gives a warning about future change of the
- default value of argument 'preserveScale' (from current TRUE to FALSE).
- The warning only appears if the argument is not specified explicitly.
-o Now using use() of R.utils where possible.
-o 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.
-o Bumped package dependencies.
+CODE REFACTORING:
+ o CLEANUP: Minor internal cleanup and restructuring.
-Version: 0.42.2 [2014-05-24]
-o Bumped package dependencies.
-Version: 0.42.1 [2014-05-05]
-o BUG FIX: pruneByHClust() for PairedPSCBS would give an error on
- "unable to find an inherited method for function 'anyMissing' for
- signature '"PairedPSCNSegments"'", unless the object contained
- bootstrap statistics. This is no longer needed. Thanks to
- Junsong Zhao, Los Angeles, CA for reporting on this.
+Version: 0.61.0 [2016-02-03]
+SIGNIFICANT CHANGES:
-Version: 0.42.0 [2014-04-25]
-o SPEEDUP: Minor speedup (a few percents) by now byte compiling the
- package by default.
-o CLEANUP: Dropped unnecessary usage of '::'.
-o Bumped package dependencies.
+ o Package now requires R (>= 3.1.2) released October 2014, because of its
+ dependency on the listenv package.
+NEW FEATURES:
-Version: 0.41.4 [2014-03-30]
-o GENERALIZATION: Now callROH() also works if paired PSCBS was done
- with only 'muN' available (and not 'betaN'). In that case, it assumes
- that all genotype confidence scores are equal.
-o Updated the ordering and the defaults of testROH() arguments to make
- it clear that 'betaN' is optional and only used if 'csN' is not given.
-o As an alternative to argument 'CT', segmentByPairedPSCBS() now accepts
- arguments 'thetaT' and 'thetaN', in case 'CT' is calculated as
- CT=2*thetaT/thetaN.
+ o segmentByPairedPSCBS() gained argument 'rho' for paired PSCBS segmentation
+ on total CNs (TCNs) and decrease-of-heterozygosity signals (DHs) as an
+ alternative to for instance TCN and allele B fractions (BAFs).
+BUG FIXES:
-Version: 0.41.3 [2014-03-29]
-o Methods no longer generates warnings on "in max(c(NA_integer_,
- NA_integer_), na.rm = TRUE) : no non-missing arguments to max;
- returning -Inf".
-o BUG FIX: In rare cases, callROH() could throw "Error in if
- (is.na(delta)) { : argument is of length zero".
+ o Segmentation using futures where not fully reproducible when known segments
+ where specified. Fixed by changing how the random number stream is set and
+ used.
-Version: 0.41.2 [2014-03-28]
-o Added argument 'preserveScale' to segmentByPairedPSCBS(), which is
- passed as is to normalizeTumorBoost() with the default being TRUE
- corresponding to the previous default behavior.
+Version: 0.60.0 [2015-11-17]
+NEW FEATURES:
-Version: 0.41.1 [2014-03-28]
-o Added unTumorBoost() to recalculating the segment means and other
- statistics for a given PairedPSCBS profile based on non-TumorBoosted
- tumor BAFs (rather than TumorBoost:ed tumor BAFs).
+ o PARALLEL: Add support for parallel processing via futures by utilizing the
+ future package. Parallel segmentation over multiple chromosomes (or known
+ segments) done by segmentByCBS() and segmentByPairedPSCBS() is enabled by
+ future::plan("multicore").
+ o REPRODUCIBILITY: Whenever argument 'seed' is given, the L'Ecuyer-CMRG stream
+ is now used to generate random numbers. For backward compatibility with
+ other types of random number generators, don't specify argument 'seed' but
+ instead use set.seed() to set the seed before calling the method.
-Version: 0.41.0 [2014-03-26]
-o Now estimateKappaByC1Density() give more informative error messages
- if it failed to identify modes for estimating the parameter.
-o Added argument 'from' to estimateKappaByC1Density().
-o BUG FIX: updateMeansC1C2() for PairedPSCBS did not handle missing
- values (=splitters) in the 'c1c2Swap' field.
-o BUG FIX: updateMeans() for PairedPSCBS and NonPairedPSCBS returned the
- incorrect DH segment levels for region in AB if adjustFor="ab" and
- likewise for segments in LOH if adjustFor="loh". This bug does *not*
- affect any of PSCBS methods themselves, because none of them utilizes
- those 'adjustFor' options.
-o Bumped package dependencies.
+CODE REFACTORING:
+ o Bump package dependencies.
-Version: 0.40.4 [2014-02-04]
-o BUG FIX: all.equal() for CBS would pass the first/dispatch argument
- to NextMethod() as 'target=target' and not as 'object=target', which
- would result in it being passed it twice both named and non-named
- where the latter would become argument 'tolerance=target' in an
- internal call to all.equal() for numerics. In recent R-devel version
- this would generate "Error in all.equal.numeric(target[[i]],
- current[[i]], check.attributes = check.attributes, : 'tolerance'
- should be numeric Calls: stopifnot ... all.equal.default ->
- all.equal.list -> all.equal -> all.equal.numeric".
+Version: 0.50.0 [2015-10-14]
-Version: 0.40.3 [2014-01-29]
-o ROBUSTNESS: Now segmentByPairedPSCBS() asserts that argument 'muN'
- is not all NAs. Similarily, if 'muN' is called from 'betaN' the
- same assertion is done after calling.
+SIGNIFICANT CHANGES:
+ o Now argument 'preserveScale' for segmentByPairedPSCBS() defaults to FALSE.
+ In the past the default has effectively been TRUE, but has given a warning
+ since v0.43.0 (June 2014) that it eventually will be changed to FALSE. Now
+ it will give a warning that it has changed, unless the option is explicitly
+ specified. This new warning will eventually be removed in a future version.
-Version: 0.40.2 [2013-12-17]
-o Now estimateDeltaCN() for CBS have the option to estimate the size
- of a copy-number unit based on the change-point magnitutes, in
- addition to the estimator based on the density of segment means.
-o BUG FIX: getChangePoints() for CBS returned empty results.
+Version: 0.45.1 [2015-09-16]
-Version: 0.40.1 [2013-12-09]
-o DOCUMENTATION: The CBS vignette referred to C1 and C2 in one of
- the code examples.
-o Bumped package dependencies.
+NEW FEATURES:
+ o More informative error messages when append() for CBS or PSCBS fail.
-Version: 0.40.0 [2013-12-07]
-o CLEANUP: No longer need for an ad hoc NAMESPACE import.
+BUG FIXES:
+ o segmentByCBS(, ..., w, knownSegments) would give internal assertion errors
+ if one of the priorly known segments would have zero data points. Thanks to
+ Kirill Tsukanov (Moscow) and Eric Talevich (UCSF) for reporting on this.
-Version: 0.39.8 [2013-12-04]
-o DOCUMENTATION: Now the vignette sections on dropping outliers
- before segmentation explains why outliers are dropped whereas in
- the original CBS publication they were shrunk ("smoothed").
- Also, added help for dropSegmentationOutliers().
+Version: 0.45.0 [2015-09-11]
-Version: 0.39.7 [2013-11-27]
-o Added callGLAO() for CBS.
-o Added encodeCalls() for 'data.frame' object returned by
- getLocusData(..., addCalls=TRUE).
-o Bumped package dependencies.
+SIGNIFICANT CHANGES:
+ o Package now requires R (>= 3.1.1) released July 2014. This allows us to use
+ BioC (>= 3.0) (October 2014).
+
+NEW FEATURES:
-Version: 0.39.6 [2013-11-23]
-o Added clearCalls() for AbstractCBS.
-o Added extractSegmentDataByLocus() for PairedPSCBS.
-o BUG FIX: estimateDeltaCN() for CBS assumed aroma.light was attached.
+ o segmentByCBS() gained argument 'avg'.
+ o Add writeWIG() for CBS objects.
-Version: 0.39.5 [2013-11-15]
-o Added estimateDeltaCN() for CBS. Added package system test.
+ o pruneByHClust() no longer gives a message about method "ward" is now named
+ "ward.D".
+ o Added skip = TRUE to report().
-Version: 0.39.4 [2013-11-14]
-o BUG FIX: callGainsAndLosses() for CBS would not estimate the median
- median CN level correctly if there were "empty" segments (e.g. gaps).
- This was/is due to a bug in segments.summary() of the DNAcopy package.
- Instead, we are now calculating the segment median levels ourselves.
- Added a system package test for callGainsAndLosses().
+BUG FIXES:
+ o plotTracks() for CBS ignored arguments 'cex', 'col' and 'meanCol' if two or
+ more chromosomes were plotted.
-Version: 0.39.3 [2013-11-05]
-o Added basic implementations of setLocusData() and setSegments()
- for AbstractCBS.
+ o joinSegments(), resetSegments() and pruneBySdUndo() gave errors for multi-
+ chromosome (>= 2) segmentation results.
+ o segmentByCBS() would ignore argument 'w' (weights) if more than one
+ chromosome was fitted.
-Version: 0.39.2 [2013-10-28]
-o Now plotTracksManyChromosomes() for PairedPSCBS also supports
- tracks "c1,c2", "c1" and "c2".
+ o tileChromosomes() for CBS returned incorrect locus data.
+ o gapsToSegments(gaps) gave an error if nrow(gaps) == 0 or contained no
+ 'chromosome' column.
-Version: 0.39.1 [2013-10-25]
-o Now plotTracksManyChromosomes() uses the locus data field 'rho'
- when plotting DH locus-level data. It only recalculates it from
- the tumor BAFs if the DH signals are not available - if so a
- warning is generated.
-o BUG FIX: The 'rho' signals returned by getLocusData(..., fields="full")
- for PairedPSCBS would have values also for homozygote SNPs.
+ o findLargeGaps() could return NULL. Now it always returns a data.frame.
+ o The report() RSP-embedded TeX templates for CBS and PairedPSCBS data did not
+ escape sample and data set names to LaTeX in all places needed.
+CODE REFACTORING:
-Version: 0.39.0 [2013-10-23]
-o Now all warnings generated by DNAcopy::CNA() are suppressed,
- including the common one on "array has repeated maploc positions".
-o Added getBootstrapLocusSets() for PairedPSCBS. Added a package
- system test for it.
-o Added argument 'subset' to applyByRegion() for PairedPSCBS.
-o Added clearBootstrapSummaries() for PairedPSCBS.
-o SPEEDUP: Added argument 'cache' to bootstrapSegmentsAndChangepoints(),
- which caches the results to file if cache=TRUE.
+ o ROBUSTNESS: Package test coverage is 62%.
+ o ROBUSTNESS: Explicitly importing core R functions.
-Version: 0.38.6 [2013-10-20]
-o Internal restructuring on how bootstrapping of segment means is done.
-o BUG FIX: plotTracks() for PairedPSCBS would use argument 'Clim'
- for 'Blim' as well, regardless of what argument 'Blim' is. This
- bug was introduced in v0.38.3.
+Version: 0.44.0 [2015-02-22]
-Version: 0.38.5 [2013-10-18]
-o BUG FIX: The CBS and Paired PSCBS report templates assumed that
- the 'R.utils' package is attached.
+ o Package now requires R (>= 3.0.3) and BioC (>= 2.13), which are from March
+ 2014 and are in fact old. It's recommended to use a more recent R version.
+DEPRECATED AND DEFUNCT:
-Version: 0.38.4 [2013-10-15]
-o CLEANUP: Removed a few unnecessary NAMESPACE imports.
-o Bumped package dependencies.
+ o CLEANUP: bootstrapDHByRegion() is defunct (was deprecated since 2013).
+CODE REFACTORING:
-Version: 0.38.3 [2013-10-14]
-o Now plotTracks() for CBS and PSCBS gives a more informative error if
- 'Clim' or 'Blim' is invalid. If using "auto" (only for CBS) and the
- limits could not be inferred due to an unknown or unset signal type,
- an informative error message reports on this as well.
-o Now the package vignettes are in vignettes/ and not in inst/doc/,
- which will not be supported by R (>= 3.1.0).
-o ROBUSTNESS: The overriding of append() to become a generic
- function does now call base::append() in the default, instead
- of copy the latter. All this will eventually be removed,
- when proper support for c, [, [[ etc. has been added everywhere.
-o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
+ o ROBUSTNESS: Package test coverage is 58%.
+ o ROBUSTNESS: Forgot to declare some S3 methods in NAMESPACE.
-Version: 0.38.2 [2013-10-13]
-o BUG FIX: While attaching the package, it could cause a cyclic
- loading of namespaces.
+ o SPEEDUP: Now using more functions of matrixStats.
-Version: 0.38.1 [2013-10-08]
-o Now getSmoothLocusData() for CBS also returns column 'count' which
- specifies the number of (finite) loci averaged over in each bin.
-o DOCUMENTATION: Vignette 'Total copy-number segmentation using CBS'
- would display the same plot as vignette 'Parent-specific copy-number
- segmentation using Paired PSCBS'.
-o DOCUMENTATION: Renamed vignette 'Paired PSCBS' to 'Parent-specific
- copy-number segmentation using Paired PSCBS'.
-o BUG FIX: tileChromosomes() for CBS did not set "tiledChromosomes"
- attribute due to a typo. This caused plotTracks() for CBS to
- horizontally misplace the plotted segment levels.
- Added a system tests for this for CBS and PairedPSCBS objects.
- Thanks to Ilari Scheinin at VUMC for reporting on this.
-o Bumped package dependencies.
+Version: 0.43.0 [2014-06-08]
+SIGNIFICANT CHANGES:
-Version: 0.38.0 [2013-09-27]
-o SPEEDUP: 'R CMD check' is now significantly faster due to
- copying of pre-generated calculations ("memoization").
- For instance, the the same segmentation tests are roughly
- 40% faster with this version compared to v0.37.2.
-o Now PSCBS imports 'R.cache' (used to only suggest it).
+ o Now segmentByPairedPSCBS() gives a warning about future change of the
+ default value of argument 'preserveScale' (from current TRUE to FALSE).
+ The warning only appears if the argument is not specified explicitly.
+ o 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.
-Version: 0.37.2 [2013-09-27]
-o SPEEDUP: Now utilizing 'matrixStats' functions in more places.
-o ROBUSTNESS: Further improved how aroma.light is handled for
- backward compatibility.
-o Bumped package dependencies.
+CODE REFACTORING:
+ o Now using use() of R.utils where possible.
-Version: 0.37.1 [2013-09-26]
-o CLEANUP: Now package avoids attaching suggested packages such as
- 'R.cache', 'aroma.light', and 'Hmisc' by only importing the set of
- functions needed via '::'. This way those packages are only loaded.
- Packages that still need to be attached are done so "quietly".
-o CLEANUP: Minor adjustments to some of the internal workarounds
- for older versions of 'matrixStats' and 'aroma.light'.
-o BUG FIX: Forgot to import several functions from 'matrixStats'.
- These went undetected because 'aroma.light' (<= 1.31.5) attaches
- the 'matrixStats'.
-o BUG FIX: segmentByPairedPSCBS() assumed 'aroma.light' was attached.
-o BUG FIX: One of the system tests assumed 'R.utils' was attached.
+ o Bumped package dependencies.
-Version: 0.37.0 [2013-09-21]
-o CLEANUP: Package no longer attaches 'R.utils', only imports it.
-o BUG FIX/WORKAROUND: For now, package attaches the 'utils' package.
- This is needed due to what appears to be a bug in how 'R.oo'
- finalizes Object:s assuming 'utils' is attached, which may not be
- the case (unless 'R.oo' itself is attached).
-o ROBUSTNESS: Now package imports only what is needed from 'DNAcopy'.
-o BUG FIX: callGNL() for PairedPSCBS used non-defined 'verbose' object.
+Version: 0.42.2 [2014-05-24]
+CODE REFACTORING:
-Version: 0.36.2 [2013-09-18]
-o DOCUMENTATION: Added vignette 'Total copy-number segmentation using CBS'.
-o ROBUSTNESS: Now package imports 'matrixStats' (previously suggested).
-o ROBUSTNESS: Now package declares S3 methods in the NAMESPACE.
-o ROBUSTNESS: Package vignettes no longer assumes that the 'R.rsp'
- package is attached.
-o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
-o WORKAROUND: For R (< 3.0.0), hclustCNs() for AbstractCBS would generate
- 'Error in rowAlls(ok) : could not find function "loadMethod"'. This
- seems to be a bug in R (< 3.0.0), which we can avoid by attaching the
- 'methods' package in hclustCNs().
-o Bumped package dependencies.
+ o Bumped package dependencies.
-Version: 0.36.1 [2013-09-10]
-o CLEANUP: Package no longer utilizes ':::'.
+Version: 0.42.1 [2014-05-05]
+BUG FIXES:
-Version: 0.36.0 [2013-08-15]
-o Made extractMinorMajorCNs() for PairedPSCBS acknowledge additional
- fields related to (C1,C2).
+ o pruneByHClust() for PairedPSCBS would give an error on "unable to find an
+ inherited method for function 'anyMissing' for signature
+ '"PairedPSCNSegments"'", unless the object contained bootstrap statistics.
+ This is no longer needed. Thanks to Junsong Zhao, Los Angeles, CA for
+ reporting on this.
-Version: 0.35.6 [2013-08-01]
-o Updated the vignettes to utilize the new R.rsp features.
+Version: 0.42.0 [2014-04-25]
+CODE REFACTORING:
-Version: 0.35.5 [2013-07-19]
-o ROBUSTNESS: Added a sanity check on the estimates of (tauA, tauB)
- when they are estimated from data in segmentByNonPairedPSCBS().
+ o Minor speedup (a few percents) by now byte compiling the package by default.
+ o CLEANUP: Dropped unnecessary usage of '::'.
-Version: 0.35.4 [2013-07-11]
-o Updated the Makefile for the vignettes and added .Rinstignore such
- that auxiliary (bib and bst) LaTeX files are not installed but
- part of the build so they are available to R CMD check, which
- is recently needed by R devel.
-o Bumped package dependencies.
+ o Bumped package dependencies.
-Version: 0.35.3 [2013-05-25]
-o Minor speedup by replacing all rm(x) with x <- NULL, cf. R-devel
- thread 'Assigning NULL to large variables is much faster than rm() -
- any reason why I should still use rm()?' on May 25, 2013.
+Version: 0.41.4 [2014-03-30]
+NEW FEATURES:
-Version: 0.35.2 [2013-05-20]
-o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
+ o GENERALIZATION: Now callROH() also works if paired PSCBS was done with only
+ 'muN' available (and not 'betaN'). In that case, it assumes that all
+ genotype confidence scores are equal.
+ o Updated the ordering and the defaults of testROH() arguments to make it
+ clear that 'betaN' is optional and only used if 'csN' is not given.
-Version: 0.35.1 [2013-05-07]
-o Now estimateDeltaCN() for PairedPSCBS adjust for the ploidy if set.
-o Added ploidy() and ploidy()<- for AbstractCBS.
-o Now tileChromosomes() no longer gives warnings on "max(i): no
- non-missing arguments to max; returning -Inf".
+ o As an alternative to argument 'CT', segmentByPairedPSCBS() now accepts
+ arguments 'thetaT' and 'thetaN', in case 'CT' is calculated as
+ CT = 2 * thetaT / thetaN.
-Version: 0.35.0 [2013-04-23]
-o SPEEDUP: Now bootstrapTCNandDHByRegion() for PairedPSCBS always
- estimates the default quantiles in addition to any requested ones.
-o SPEEDUP: Made bootstrapTCNandDHByRegion() much faster by adding
- use.names=FALSE to two internal unlist() statements.
-o BUG FIX: updateMeans() for PairedPSCBS and NonPairedPSCBS could
- include a signal from a neighboring segment when averaging, iff
- that signal was located at the exact locus of the change point.
- Thanks Ingrid L�nnstedt (WEHI) for reporting on this.
+Version: 0.41.3 [2014-03-29]
+NEW FEATURES:
-Version: 0.34.9 [2013-04-22]
-o Utilizing new startupMessage() of R.oo.
-o BUG FIX: updateMeans() would not always preserve the originally
- specified segment-mean level estimator, if different from a
- (sample) mean estimator, e.g. avgDH="median". This could result
- in for instance callAB() failing on internal sanity checks.
-o BUG FIX: Segment levels drawn by plotTracks() would have incorrect
- genomic locations for chromosome 2 and beyond. This bug was
- introduced in v0.34.7.
+ o Methods no longer generates warnings on "in max(c(NA_integer_, NA_integer_),
+ na.rm = TRUE) : no non-missing arguments to max; returning -Inf".
+BUG FIXES:
-Version: 0.34.8 [2013-04-20]
-o CLEANUP: Removed previously deprecated methods for AbstractCBS.
+ o In rare cases, callROH() could throw "Error in if (is.na(delta)) { :
+ argument is of length zero".
-Version: 0.34.7 [2013-04-18]
-o Added more arguments to plotTracks().
-o Now drawLevels() and drawConfidenceBands() for CBS and PairedPSCBS
- also works for multiple chromosomes.
-o One of the system tests for segmentByPairedPSCBS() failed
- in the case when the data was downsampled (in order to meet
- the CRAN requirements). The workaround is to use a fix deltaAB
- parameter in that case.
-o BUG FIX: Internal calcStatsForCopyNeutralABs() would give an
- error if there was exactly two AB segments.
+Version: 0.41.2 [2014-03-28]
+NEW FEATURES:
-Version: 0.34.6 [2013-04-11]
-o BUG FIX: plotTracks(fit, callLoci=TRUE) would color loci incorrectly
- if more than one chromosome are plotted.
+ o Added argument 'preserveScale' to segmentByPairedPSCBS(), which is passed as
+ is to normalizeTumorBoost() with the default being TRUE corresponding to the
+ previous default behavior.
-Version: 0.34.5 [2013-04-09]
-o ROBUSTNESS: Now callROH() gives an informative error if called
- on a NonPairedPSCBS object.
+Version: 0.41.1 [2014-03-28]
+NEW FEATURES:
-Version: 0.34.4 [2013-04-05]
-o Added more end-user control to plotTracks().
+ o Added unTumorBoost() to recalculating the segment means and other statistics
+ for a given PairedPSCBS profile based on non-TumorBoosted tumor BAFs (rather
+ than TumorBoost:ed tumor BAFs).
-Version: 0.34.3 [2013-04-04]
-o Now package builds with both R.rsp (< 0.9.1) and R.rsp (>= 0.9.1).
+Version: 0.41.0 [2014-03-26]
+NEW FEATURES:
-Version: 0.34.2 [2013-03-28]
-o Updated callGainNeutralLoss(), which now by default utilizes
- callCopyNeutral().
+ o Now estimateKappaByC1Density() give more informative error messages if it
+ failed to identify modes for estimating the parameter.
+ o Added argument 'from' to estimateKappaByC1Density().
-Version: 0.34.1 [2013-03-21]
-o Updated the report generator and its RSP templates.
-o DOCUMENTATION: Clarified in the PSCBS vignette that the NTCN
- caller is under development, experimental.
-o SPEEDUP: Made dropChangePoints() faster by only updating the
- segment statistics/means at the very end.
+BUG FIXES:
+ o updateMeansC1C2() for PairedPSCBS did not handle missing values (=splitters)
+ in the 'c1c2Swap' field.
-Version: 0.34.0 [2013-03-19]
-o CALLING: Defined a formal hypothesis test for how segments are called
- copy-neutral in TCN (NTCN), with the null hypothesis being that a
- segment is NTCN. In order for a segment to not be NTCN, its confidence
- interval has to be completely outside the null region. This changed
- how callCopyNeutralByTCNofAB() for PairedPSCBS calls segments; it is
- now a bit more conservative in rejecting NTCN.
+ o updateMeans() for PairedPSCBS and NonPairedPSCBS returned the incorrect DH
+ segment levels for region in AB if adjustFor = "ab" and likewise for
+ segments in LOH if adjustFor = "loh". This bug does *not* affect any of
+ PSCBS methods themselves, because none of them utilizes those 'adjustFor'
+ options.
+CODE REFACTORING:
-Version: 0.33.4 [2013-03-19]
-o ROBUSTNESS: Now calcStatsForCopyNeutralABs() for PairedPSCBS does
- a better job in identifying the TCN mode of the AB segments.
-o Added argument 'flavor' to findNeutralCopyNumberState() specifying
- how to identify the main mode of the AB segments.
-o VISUALIZATION: Now plotTracks() for PairedPSCBS displays thresholds
- for calling AB, LOH and and NTCN.
+ o Bumped package dependencies.
-Version: 0.33.3 [2013-03-12]
-o DOCUMENTATION: Documented 'tauA' and 'tauB' in the help for
- segmentByNonPairedPSCBS().
+Version: 0.40.4 [2014-02-04]
+BUG FIXES:
-Version: 0.33.2 [2013-03-09]
-o Added getLocusData() for PairedPSCBS and NonPairedPSCBS.
-o Added an Authors at R field to the DESCRIPTION.
-o DOCUMENTATION: Updated the vignettes and the report templates to
- utilize the new ggplot2 themes - ggplot2 no longer gives a
- warning on using deprecated functions.
-o Now report() for AbstractCBS also includes files listed in the
- optional file '.install_extras' of the source RSP template
- directory. The same filename is used by 'R CMD build/check' for
- including additional source files needed to build the vignettes.
+ o all.equal() for CBS would pass the first/dispatch argument to NextMethod()
+ as 'target = target' and not as 'object = target', which would result in it
+ being passed it twice both named and non-named where the latter would become
+ argument 'tolerance = target' in an internal call to all.equal() for
+ numerics. In recent R-devel version this would generate "Error in
+ all.equal.numeric(target[[i]], current[[i]], check.attributes =
+ check.attributes, : 'tolerance' should be numeric Calls: stopifnot ...
+ all.equal.default -> all.equal.list -> all.equal -> all.equal.numeric".
-Version: 0.33.1 [2013-03-07]
-o Relaxed the internal precision tests of testROH(). This was done
- in response to the CRAN farm lowering its precision on some hosts.
-o DOCUMENTATION: Preparing package vignettes for the upcoming
- R 3.0.0 support for non-Sweave vignettes.
+Version: 0.40.3 [2014-01-29]
+NEW FEATURES:
-Version: 0.33.0 [2013-03-05]
-o Added argument 'typeOfWeights' to estimateKappaByC1Density() for
- PairedPSCBS, and hence indirectly to estimateKappa(). The default
- is typeOfWeights="dhNbrOfLoci", which may give too much overall
- weight to very long segments causing the estimator to fail when
- there are only a few number of "C1 = 0" segments. An alternative
- is to use typeOfWeights="sqrt(dhNbrOfLoci)".
+ o ROBUSTNESS: Now segmentByPairedPSCBS() asserts that argument 'muN' is not
+ all NAs. Similarily, if 'muN' is called from 'betaN' the same assertion is
+ done after calling.
-Version: 0.32.6 [2013-03-04]
-o DOCUMENTATION: Updated the help usage section for all static methods.
+Version: 0.40.2 [2013-12-17]
+NEW FEATURES:
-Version: 0.32.5 [2013-02-09]
-o Added a VignetteBuilder field to DESCRIPTION.
-o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS did not
- bootstrap from all available loci when calculating total CNs
- statistics, iff the segment had been called run-of-homozygosity
- (ROH). Internal validation tests caught this. Thanks to Oscar Rueda
- at the Cancer Research UK Cambridge Institute for reporting on this.
+ o Now estimateDeltaCN() for CBS have the option to estimate the size of a
+ copy-number unit based on the change-point magnitutes, in addition to the
+ estimator based on the density of segment means.
+BUG FIXES:
-Version: 0.32.4 [2013-02-07]
-o Improved some verbose outputs of bootstrapTCNandDHByRegion().
+ o getChangePoints() for CBS returned empty results.
-Version: 0.32.3 [2013-02-05]
-o Now pruneByHClust() drops any existing segment calls and quantile
- mean-level estimates.
+Version: 0.40.1 [2013-12-09]
+DOCUMENTATION:
-Version: 0.32.2 [2013-02-01]
-o Added resetSegments() for AbstractCBS, which drops extra segments
- columns (e.g. bootstrap statistics and calls) except those
- obtained from the segment algorithm.
-o ROBUSTNESS: Now aroma.light is explicitly required in cases
- where it is needed.
-o DOCUMENTATION: Added a paragraph on avgDH="median" to the PSCBS
- vignette's 'Experimental' section.
+ o The CBS vignette referred to C1 and C2 in one of the code examples.
+CODE REFACTORING:
-Version: 0.32.1 [2013-02-01]
-o BUG FIX: segmentByPairedPSCBS(..., avgDH="median") only worked for
- single-chromosome data. Same for avgTCN="median". Thanks Ritu Roy
- at UCSF for reporting on this.
+ o Bumped package dependencies.
-Version: 0.32.0 [2013-01-16]
-o Added arguments 'avgTCN' and 'avgDH' to segmentByPairedPSCBS().
-o Now updateMeans() and updateMeansTogether() methods can estimate
- the mean levels either by the sample mean or the median.
+Version: 0.40.0 [2013-12-07]
+CODE REFACTORING:
-Version: 0.31.0 [2013-01-05]
-o CLEANUP: Now packages R.methodsS3 and R.oo are only imported.
-o CLEANUP: Package no longer explicitly imports digest.
+ o CLEANUP: No longer a need for an ad-hoc NAMESPACE import.
-Version: 0.30.0 [2012-11-05]
-o GENERALIZATION: Now bootstrapTCNandDHByRegion() works for more
- "flavors", e.g the default ('tcn') used by segmentByNonPairedPSCBS().
+Version: 0.39.8 [2013-12-04]
+DOCUMENTATION:
-Version: 0.29.9 [2012-11-05]
-o DOCUMENTATION FIX: example(segmentByNonPairedPSCBS) was for
- the paired case.
-o CRAN POLICY: Further speed up of examples such that they run faster
- with R CMD check.
+ o Now the vignette sections on dropping outliers before segmentation explains
+ why outliers are dropped whereas in the original CBS publication they were
+ shrunk ("smoothed"). Also, added help for dropSegmentationOutliers().
-Version: 0.29.8 [2012-11-04]
-o CLEANUP: Replaced all whichVector() with which(), because the
- latter is now the fastest again.
+Version: 0.39.7 [2013-11-27]
+NEW FEATURES:
-Version: 0.29.7 [2012-11-03]
-o Updated deprecated ggplot2 functions in the RSP reports.
+ o Added callGLAO() for CBS.
+ o Added encodeCalls() for 'data.frame' object returned by getLocusData(...,
+ addCalls = TRUE).
-Version: 0.29.6 [2012-11-01]
-o Bumped package dependencies.
-o CRAN POLICY: Made the examples run faster for R CMD check.
+CODE REFACTORING:
+ o Bumped package dependencies.
-Version: 0.29.5 [2012-10-16]
-o ROBUSTNESS/BUG FIX: 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: 0.39.6 [2013-11-23]
-Version: 0.29.4 [2012-09-23]
-o Now plotTracks() [and plotTracksManyChromosomes()] draws segment levels
- such that it is easier to see them even when they are overlapping.
+NEW FEATURES:
+ o Added clearCalls() for AbstractCBS.
-Version: 0.29.3 [2012-09-21]
-o SPEEDUP: By default bootstrapTCNandDHByRegion() for PairedPSCBS no
- longer do sanity checks within the bootstrap loop. This significantly
- speed up the method. To run checks, use argument .debug=TRUE.
- In addition, the callNnn() methods that need to call this method,
- does it by decreasing the amount of verbose output substantially,
- which in turn speeds up the process a fair bit.
-o Now getSegments(..., splitters=TRUE) for CBS and PSCBS inserts NA
- rows wherever there is a "gap" between segments. A "gap" is when
- two segments are not connected (zero distance).
-o ROBUSTNESS: Now append() for CBS and PSCBS drops column 'length'
- from 'knownSegments', iff it exists.
-o Now nbrOfChangePoints() for AbstractCBS calculates only change points
- of connected neighboring segments.
-o BUG FIX: seqOfSegmentsByDP() for AbstractCBS would not handle empty
- segments, which could occur if 'knownSegments' for instance included
- centromere gaps.
-o BUG FIX: segmentByCBS(... knownSegments) could return segments for
- chromosome 0 even though it did not exist in the input data.
+ o Added extractSegmentDataByLocus() for PairedPSCBS.
+BUG FIXES:
-Version: 0.29.2 [2012-09-18]
-o REPORT: Now report() for AbstractCBS looks for the RSP template in
- templates/, and as a backup in templates,PSCBS/. If the latter does
- not exist, it is automatically created as a soft link to templates/
- of the PSCBS package. This allows anyone to create their own
- customized copy (in templates/) of the default PSCBS RSP report.
-o REPORT: Now report(fit, ..., rspTags) for AbstractCBS looks for the
- RSP template named <className>(,<rspTags>),report.tex.rsp, where
- className is class(fit)[1] and argument 'rspTags' is an optional
- comma-separated character string/vector. This makes it possible
- to have different types of report for the same class of objects.
-o REPORT: Added argument 'force' to report() for AbstractCBS. This
- will copy the RSP template files again, although they are already
- in reports/ output directory.
+ o estimateDeltaCN() for CBS assumed aroma.light was attached.
-Version: 0.29.1 [2012-09-15]
-o Added argument 'dropMissingCT' to segmentByPairedPSCBS().
+Version: 0.39.5 [2013-11-15]
+NEW FEATURES:
-Version: 0.29.0 [2012-09-14]
-o Added trial version of pruneByDP() for AbstractCBS.
+ o Added estimateDeltaCN() for CBS. Added package system test.
-Version: 0.28.6 [2012-09-13]
-o Now tileChromosomes() also adjusts 'knownSegments'.
-o Added argument 'dropGaps' to gapsToSegments().
-o Updated all.equal() for AbstractCBS to compare locus-level data,
- segments, and other fields.
+Version: 0.39.4 [2013-11-14]
+BUG FIXES:
-Version: 0.28.5 [2012-09-13]
-o SPEEDUP: Now segmentByCBS(..., undo=+Inf) returns much faster, which
- is possible because there is no need to identify new change points.
+ o callGainsAndLosses() for CBS would not estimate the median median CN level
+ correctly if there were "empty" segments (e.g. gaps). This was/is due to a
+ bug in segments.summary() of the DNAcopy package. Instead, we are now
+ calculating the segment median levels ourselves. Added a system package
+ test for callGainsAndLosses().
-Version: 0.28.4 [2012-09-13]
-o CONSISTENCY FIX: Changed the behavior of extreme values of argument
- 'undo' to segmentByCBS() such that 'undo=0' (was 'undo=+Inf') now
- means that it will not ask DNAcopy::segment() to undo the segmentation,
- and such that 'undo=+Inf' means that no changepoints will be identified.
- The latter case allows you to effectively skip the segmentation but
- still calculate all the CBS statistics across a set of known segments
- via segmentByCBS(..., undo=+Inf, knownSegments=knownSegments).
- Arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS() are
- adjusted analogously. Corresponding system tests were added.
+Version: 0.39.3 [2013-11-05]
+NEW FEATURES:
-Version: 0.28.3 [2012-08-30]
-o Updated code and Rd cross reference to use the 'matrixStats'
- package for weightedMedian(), which used to be in 'aroma.light'.
+ o Added basic implementations of setLocusData() and setSegments() for
+ AbstractCBS.
-Version: 0.28.2 [2012-08-20]
-o BUG FIX: segmentByNonPairedPSCBS() forgot to specify namespace
- aroma.light when trying to call findPeaksAndValleys().
+Version: 0.39.2 [2013-10-28]
+NEW FEATURES:
-Version: 0.28.1 [2012-08-15]
-o Minor grammatical corrections of the Paired PSCBS vignette.
+ o Now plotTracksManyChromosomes() for PairedPSCBS also supports tracks
+ "c1,c2", "c1", and "c2".
-Version: 0.28.0 [2012-07-22]
-o Added argument 'minLength' to gapsToSegments(). The default is no
- longer to drop zero-length (minLength == -1L) segments, because
- if (and only if) such a segment contains a locus, then segmentByNnn()
- will currently generate an (internal) error.
-o GENERALIZATION/BUG FIX: Now segmentByPairedPSCBS() drops loci for
- which CT is missing (regardless of betaT). For instance, in rare cases
- when the reference (e.g. the normal) is missing, then it may be that
- CT is missing while betaT is not.
+Version: 0.39.1 [2013-10-25]
+NEW FEATURES:
-Version: 0.27.4 [2012-07-22]
-o Now verbose output of segmentByPairedPSCBS() specifies region
- ranges with greater precision.
+ o Now plotTracksManyChromosomes() uses the locus data field 'rho' when
+ plotting DH locus-level data. It only recalculates it from the tumor BAFs
+ if the DH signals are not available - if so a warning is generated.
+BUG FIXES:
-Version: 0.27.3 [2012-07-10]
-o DOCUMENTATION: Minor updates to the Paired PSCBS vignettes.
-o CLEANUP: One redundancy tests relied on a non-critical function
- that will be removed in R.utils 1.16.0 (now in R.devices 2.1.1).
+ o The 'rho' signals returned by getLocusData(..., fields = "full") for
+ PairedPSCBS would have values also for homozygote SNPs.
-Version: 0.27.2 [2012-07-08]
-o Updated package dependencies.
+Version: 0.39.0 [2013-10-23]
+NEW FEATURES:
-Version: 0.27.1 [2012-07-02]
-o Now we refer to "copy neutral" segments as "neutral TCN" segments
- with acronym 'NTCN'. The corresponding column in the segmentation
- results are labeled correspondingly. The Paired PSCBS vignette
- was updated accordingly.
+ o Now all warnings generated by DNAcopy::CNA() are suppressed, including the
+ common one on "array has repeated maploc positions".
+ o Added getBootstrapLocusSets() for PairedPSCBS. Added a package system test
+ for it.
-Version: 0.27.0 [2012-06-24]
-o (An update that should be ignored)
-o DOCUMENTATION: Some grammar corrections of the 'Paired PSCBS' vignette.
+ o Added argument 'subset' to applyByRegion() for PairedPSCBS.
+ o Added clearBootstrapSummaries() for PairedPSCBS.
-Version: 0.26.1 [2012-06-05]
-o Now segmentByCBS() for data frame:s does a better job identifying
- the CN signals.
+ o SPEEDUP: Added argument 'cache' to bootstrapSegmentsAndChangepoints(), which
+ caches the results to file if cache = TRUE.
-Version: 0.26.0 [2012-06-03]
-o DOCUMENTATION: Added details to the Paired PSCBS vignette on how
- to call segments that are copy neutral (typically diploid).
-o Now argument 'delta' for callCopyNeutralByTCNofAB() of PairedPSCBS
- is calculated via estimateDeltaCN(), which estimates the width
- of the acceptance regions, used for calling copy neutral states,
- to be a function of the normal contamination.
+Version: 0.38.6 [2013-10-20]
+BUG FIXES:
-Version: 0.25.3 [2012-06-03]
-o BUG FIX: all.equal(target, current) for CBS objects would give an
- error if either 'target' or 'current' had zero segments.
+ o plotTracks() for PairedPSCBS would use argument 'Clim' for 'Blim' as well,
+ regardless of what argument 'Blim' is. This bug was introduced in v0.38.3.
+CODE REFACTORING:
-Version: 0.25.2 [2012-05-30]
-o Added writeSegments() for DNAcopy objects.
-o BUG FIX: as.CNA() for DNAcopy added incorrect chromosome splitters.
-o BUG FIX: as.CNA() for DNAcopy would ignore argument 'sample' and
- always return the first sample.
+ o Internal restructuring on how bootstrapping of segment means is done.
-Version: 0.25.1 [2012-05-30]
-o DOCUMENTATION: Added details to the Paired PSCBS vignette on how
- to tune the various callers.
-o Now callROH() records parameter 'deltaROH' in the results.
-o BUG FIX: callLOH(..., force=TRUE) would append multiple 'lohCall'
- columns, if called multiple times.
+Version: 0.38.5 [2013-10-18]
+BUG FIXES:
-Version: 0.25.0 [2012-04-20]
-o Added a trial (very much true) version of segmentByNonPairedPSCBS().
+ o The CBS and Paired PSCBS report templates assumed that the 'R.utils' package
+ is attached.
-Version: 0.24.0 [2012-04-20]
-o Now it is possible to skip the DH segmentation in Paired PSCBS, i.e.
- segmentByPairedPSCBS(..., flavor="tcn").
+Version: 0.38.4 [2013-10-15]
+CODE REFACTORING:
-Version: 0.23.2 [2012-04-20]
-o BUG FIX: segmentByPairedPSCBS() would throw "error in `$<-.data.frame
- `(`*tmp*`, "rho" ..." if some loci had unknown genomic positions.
+ o CLEANUP: Removed a few unnecessary NAMESPACE imports.
+ o Bumped package dependencies.
-Version: 0.23.1 [2012-04-20]
-o Added RSP report for CBS objects (adopted from ditto for PairedPSCBS).
-o DOCUMENTATION: Updated the 'Paired PSCBS' vignette.
+Version: 0.38.3 [2013-10-14]
-Version: 0.23.0 [2012-03-20]
-o DOCUMENTATION: Added a package vignette.
+NEW FEATURES:
+ o Now plotTracks() for CBS and PSCBS gives a more informative error if 'Clim'
+ or 'Blim' is invalid. If using "auto" (only for CBS) and the limits could
+ not be inferred due to an unknown or unset signal type, an informative error
+ message reports on this as well.
-Version: 0.22.2 [2012-02-29]
-o BUG FIX: plotTracks(..., add=TRUE) for PairedPSCBS would add TCNs
- when BAFs and DHs were intended.
+CODE REFACTORING:
+ o Now the package vignettes are in vignettes/ and not in inst/doc/, which will
+ not be supported by R (>= 3.1.0).
-Version: 0.22.1 [2012-02-28]
-o Updated package dependencies to R.rsp (>= 0.7.3) so that
- report() for PairedPSCBS no longer require non-public packages.
-o Now it is possible to turn off usage of the alpha channel in
- plots generated by report(), which can be handy on systems where
- the default PNG device does not support the alpha channel.
- Example: setOption("PSCBS::report/useAlphaChannel", FALSE).
+ o ROBUSTNESS: The overriding of append() to become a generic function does now
+ call base::append() in the default, instead of copy the latter. All this
+ will eventually be removed, when proper support for c, [, [[ etc. has been
+ added everywhere.
+ o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
-Version: 0.22.0 [2012-02-27]
-o Added report() for PairedPSCBS.
+Version: 0.38.2 [2013-10-13]
-Version: 0.21.0 [2012-02-27]
-o Added argument 'fields' to getLocusData() for PairedPSCBS.
-o Added renameChromosomes() to AbstractCBS.
+BUG FIXES:
+ o While attaching the package, it could cause a cyclic loading of namespaces.
-Version: 0.20.0 [2012-02-26]
-o Added alpha version of callGainNeutralLoss() for PairedPSCBS,
- which certainly will be updated in the future. This caller
- is tested by the system tests.
-o Added dropChangePoints() for AbstractCBS.
-o Added some internal utility functions for PairedPSCBS taken
- from the aroma.cn package. Some of these may become public
- later, but for they should be considered internal.
-o ROBUSTNESS: Added more sanity checks validating the correctness
- of what is returned by extractSegments() for CBS and PairedPSCBS.
-o BUG FIX: extractSegments() for PairedPSCBS would return incorrect
- row indices, more precisely, overlapping data chunks.
-o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would resample
- from a subset of the intended TCNs, iff the DH mean was non-finite
- while there were still heterozygous SNPs. This introduced a bias in
- the estimates, which was neglectable for large segments, but for very
- small segments (a few loci) it could be relatively large.
+Version: 0.38.1 [2013-10-08]
-Version: 0.19.8 [2012-02-23]
-o ROBUSTNESS: Package now explicitly depends on 'utils'.
+NEW FEATURES:
+ o Now getSmoothLocusData() for CBS also returns column 'count' which specifies
+ the number of (finite) loci averaged over in each bin.
-Version: 0.19.7 [2012-02-22]
-o BUG FIX: findLargeGaps() did not handle missing values for
- argument 'chromosome'.
-o BUG FIX: segmentByCBS(..., knownSegments=knownSegments) would
- incorrectly throw a sanity-check exception if 'knownSegments'
- contains a segment with 'start' and 'stop' positions being equal.
-o BUG FIX: Argument 'calls' of plotTracks() for PairedPSCBS was ignored
- if more than one chromosome was plotted.
+DOCUMENTATION:
+ o Vignette 'Total copy-number segmentation using CBS' would display the same
+ plot as vignette 'Parent-specific copy-number segmentation using Paired
+ PSCBS'.
-Version: 0.19.6 [2012-01-24]
-o ROBUSTNESS: Now getCallStatistics() for CBS asserts that calls have
- been made. If not, an exception is thrown.
+ o Renamed vignette 'Paired PSCBS' to 'Parent-specific copy-number segmentation
+ using Paired PSCBS'.
+BUG FIXES:
-Version: 0.19.5 [2012-01-21]
-o DOCUMENTATION: Added details to the help of callLOH() and callAB() on
- the difference between (AB,LOH)=(TRUE,FALSE) and (AB,LOH)=(TRUE,NA).
-o Corrected some of verbose messages of estimateDeltaLOHByMinC1ForNonAB()
- for PairedPSCBS objects.
+ o tileChromosomes() for CBS did not set "tiledChromosomes" attribute due to a
+ typo. This caused plotTracks() for CBS to horizontally misplace the plotted
+ segment levels. Added a system tests for this for CBS and PairedPSCBS
+ objects. Thanks to Ilari Scheinin at VUMC for reporting on this.
+CODE REFACTORING:
-Version: 0.19.4 [2012-01-10]
-o Now example(segmentByPairedPSCBS) and the system tests that are run
- by R CMD check are tuned to (by default) run much faster by segmenting
- using fewer data points and bootstrapping using fewer samples. This
- update was done to meet the new CRAN policy. By setting environment
- variable _R_CHECK_FULL_ to '1' the full data set is used instead.
+ o Bumped package dependencies.
-Version: 0.19.3 [2012-01-09]
-o ROBUSTNESS: Now extractSegments() for PairedPSCBS gives an informative
- error message that it is not supported if CNs were segmented using
- flavor "tcn,dh".
-o BUG FIX: postsegmentTCN() for PairedPSCBS could generate an invalid
- 'tcnSegRows' matrix, where the indices for two consecutive segments
- would overlap, which is invalid. Thanks to Minya Pu for reporting
- on failed sanity check related to this.
+Version: 0.38.0 [2013-09-27]
+CODE REFACTORING:
-Version: 0.19.2 [2011-12-29]
-o ROBUSTNESS: Explicitly added 'digest' to the list of suggested packages.
+ o SPEEDUP: 'R CMD check' is now significantly faster due to copying of
+ pre-generated calculations ("memoization"). For instance, the the same
+ segmentation tests are roughly 40% faster compared to version 0.37.2.
+ o Now PSCBS imports 'R.cache' (used to only suggest it).
-Version: 0.19.1 [2011-12-13]
-o Added support for callGainsAndLosses(..., method="ucsf-dmad")
- of CBS objects.
+Version: 0.37.2 [2013-09-27]
-Version: 0.19.0 [2011-12-12]
-o Added optional argument 'indices' to getLocusData() to be able
- to retrieve the locus-level data as indexed by input data.
-o BUG FIX: Now gapsToSegments() gave invalid segments for chromosomes
- with more than one gap. Now gapsToSegments() validates argument
- 'gaps' and asserts that it returns non-overlapping segments.
-o DOCUMENTATION: Clarified in help("segmentByCBS") how missing
- values are dealt with.
+CODE REFACTORING:
+ o SPEEDUP: Now utilizing 'matrixStats' functions in more places.
-Version: 0.18.2 [2011-12-07]
-o Now plotTracks() for CBS always returns an invisible object.
-o BUG FIX: pruneBySdUndo() for CBS did not work with more than
- one array.
+ o ROBUSTNESS: Further improved how aroma.light is handled for backward
+ compatibility.
+ o Bumped package dependencies.
-Version: 0.18.1 [2011-12-03]
-o Added drawChangePoints() for AbstractCBS.
-o Now pruneByHClust() for AbstractCBS updates the segment means.
-o Added writeSegments() for PSCBS object.
-o Now print() for AbstractCBS returns getSegments(..., simplify=TRUE).
-o Added argument 'simplify' to getSegments().
-o Added arguments 'name', 'tags' and 'exts' to writeSegments() and
- writeLocusData() and dropped 'filename'.
+Version: 0.37.1 [2013-09-26]
-Version: 0.18.0 [2011-11-28]
-o Added pruneByHClust() for AbstractCBS, with implementation
- for CBS and PairedPSCBS.
-o extractCNs() for CBS would not return a matrix but a data.frame.
-o BUG FIX: extractTotalCNs() for CBS would give an error.
+CODE REFACTORING:
+ o CLEANUP: Now package avoids attaching suggested packages such as 'R.cache',
+ 'aroma.light', and 'Hmisc' by only importing the set of functions needed via
+ '::'. This way those packages are only loaded. Packages that still need to
+ be attached are done so "quietly".
-Version: 0.17.4 [2011-11-26]
-o Added argument 'updateMeans=TRUE' to callROH() for PairedPSCBS.
-o Now bootstrapTCNandDHByRegion() for PairedPSCBS preserves NAs
- for DH and (C1,C2) quantiles, if the DH mean level is NA, which
- can happen when a segment is called ROH. This also makes sure
- that a segment called ROH will not be called AB.
-o An internal sanity check of bootstrapTCNandDHByRegion() for
- PairedPSCBS would give an error if DH mean levels had been set
- to NA for segments called ROH.
+ o CLEANUP: Minor adjustments to some of the internal workarounds for older
+ versions of 'matrixStats' and 'aroma.light'.
+BUG FIXES:
-Version: 0.17.3 [2011-11-24]
-o Added callSegmentationOutliers() and dropSegmentationOutliers()
- for data frames.
-o CLEANUP: Renamed field 'position' of the example data to 'x'.
- This helps us clean up some of the examples.
-o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would give
- an error, if a segment did not have any TCN signals, which can
- occur when known segments are specified for Paired PSCBS.
+ o Forgot to import several functions from 'matrixStats'. These went undetected
+ because 'aroma.light' (<= 1.31.5) attaches the 'matrixStats'.
+ o segmentByPairedPSCBS() assumed 'aroma.light' was attached.
-Version: 0.17.2 [2011-11-22]
-o Added findLargeGaps() and gapsToSegments().
+ o One of the system tests assumed 'R.utils' was attached.
-Version: 0.17.1 [2011-11-21]
-o BUG FIX: The internal sanity check of testROH() on weights was
- slightly too conservative (required to high precision) when it
- came to asserting that the sum of the weights equals one.
-o BUG FIX: resegment() for PairedPSCBS called segmentByCBS()
- instead of segmentByPairedPSCBS().
+Version: 0.37.0 [2013-09-21]
+BUG FIXES:
-Version: 0.17.0 [2011-11-19]
-o GENERALIZATION: Now it is possible to run Paired PSCBS (without
- TumorBoost) when only genotypes but not BAFs are available for the
- matched normal.
+ o WORKAROUND: For now, package attaches the 'utils' package. This is needed
+ due to what appears to be a bug in how 'R.oo' finalizes Object:s assuming
+ 'utils' is attached, which may not be the case (unless 'R.oo' itself is
+ attached).
+ o callGNL() for PairedPSCBS used non-defined 'verbose' object.
-Version: 0.16.3 [2011-11-17]
-o Added resegment() for CBS and PairedPSCBS for easy resegmentation.
-o Adjusted segmentByCBS() such that it can handle 'knownSegments'
- with chromosome boundaries given as -Inf and +Inf.
-o Now argument 'mar' for plotTracks() defaults to NULL.
-o ROBUSTNESS: Added redundancy tests for segmentByCBS() and
- segmentByPairedPSCBS() with argument 'knownSegments'.
-o ROBUSTNESS: Now segmentByCBS() does more validation of 'knownSegments'.
-o FIX: extractRegions() for AbstractCBS would also show verbose output.
-o BUG FIX: Now argument/parameter 'seed' is correctly preserved by
- segmentByCBS(). So is 'tbn' for segmentByPairedPSCBS().
-o BUG FIX: segmentByPairedPSCBS() would give an error when trying to
- segment DH if the TCN segment contains no data points, which could
- happen if 'knownSegments' specifies an empty segment, e.g. centromere.
-o BUG FIX: extractSegments() for CBS would throw an error when
- there were multiple chromosomes.
+CODE REFACTORING:
+ o CLEANUP: Package no longer attaches 'R.utils', only imports it.
-Version: 0.16.2 [2011-11-16]
-o Now segmentByCBS(..., w) stores weights 'w', if given, in the
- locus-level data table of the returned CBS object.
-o Added pruneBySdUndo() for CBS, which does what undo.splits="sdundo"'
- for DNA::segment(), but on the already segmented results.
-o Now updateMeans() uses locus-specific weights, iff available.
-o Added updateBoundaries() for CBS to update (start,stop) per segment.
-o CORRECTNESS: Now updateMeans() for CBS identifies loci via internal
- 'segRows' field and no longer by locations of segment boundaries,
- which gave slightly incorrect estimates for "tied" loci.
+ o ROBUSTNESS: Now package imports only what is needed from 'DNAcopy'.
-Version: 0.16.1 [2011-11-15]
-o Now more segmentation parameters are stored in the CBS object.
-o SPEEDUP: Now segmentByCBS() will use memoization to retrieve
- so called "sequential boundaries for early stopping", iff any of
- the DNAcopy::segment() arguments 'alpha', 'nperm' and 'eta' are
- specified. See also DNAcopy::getbdry().
-o Added method="DNAcopy" to estimateStandardDeviation() for CBS, which
- estimates the std. dev. using DNAcopy:::trimmed.variance().
-o BUG FIX: extractSegments() for CBS would throw an error, because in
- most cases it would created a corrupt internal 'segRows' field.
+Version: 0.36.2 [2013-09-18]
+DOCUMENTATION:
-Version: 0.16.0 [2011-11-12]
-o Added argument 'oma' and 'mar' to plotTracksManyChromosomes() for
- PairedPSCBS for setting graphical parameters when 'add' == FALSE.
-o Added callROH().
-o Added arguments 'from' and 'adjustFor' to updateMeans().
+ o Added vignette 'Total copy-number segmentation using CBS'.
+ o WORKAROUND: For R (< 3.0.0), hclustCNs() for AbstractCBS would generate
+ 'Error in rowAlls(ok) : could not find function "loadMethod"'. This seems to
+ be a bug in R (< 3.0.0), which we can avoid by attaching the 'methods'
+ package in hclustCNs().
-Version: 0.15.5 [2011-11-04]
-o BUG FIX: extractSegment() for AbstractCBS would give an error,
- because it called itself instead of extractSegments().
+CODE REFACTORING:
+ o ROBUSTNESS: Now package imports 'matrixStats' (previously suggested).
-Version: 0.15.4 [2011-10-30]
-o Added save() and load() methods to AbstractCBS, which are wrappers
- for saveObject() and loadObject() that assert the correct class
- structure. Also, the load() method will automatically update the
- class hierarchy for CBS and PairedPSCBS objects that were saved
- before adding class AbstractCBS.
+ o ROBUSTNESS: Now package declares S3 methods in the NAMESPACE.
+ o ROBUSTNESS: Package vignettes no longer assumes that the 'R.rsp' package is
+ attached.
-Version: 0.15.3 [2011-10-23]
-o BUG FIX: callAmplifications() for CBS generated an error, if
- more than one chromosome were called.
-o BUG FIX: The length of a segment must be defined as 'end-start'
- and not 'end-start+1' so that the the total length of all segments
- adds up correctly.
-o BUG FIX: highlightArmCalls() for CBS did not handle empty chromosomes.
-o BUG FIX: getCallStatisticsByArms() for CBS would thrown a error if
- argument 'genomeData' did not contain exactly the same chromosomes
- as in the CBS object.
+ o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
+ o Bumped package dependencies.
-Version: 0.15.2 [2011-10-21]
-o Added mergeThreeSegments() to AbstractCBS.
-o BUG FIX: Recent updates caused segmentByPairedPSCBS(data) not to
- work when 'data' is a data frame.
+Version: 0.36.1 [2013-09-10]
-Version: 0.15.1 [2011-10-21]
-o By setting 'start' and 'end' to NAs in 'knownSegments' (chromosome must
- still be specified), it is possible to insert an empty segment that
- disconnects the two flanking segments, e.g. centromere and the two arms.
+CODE REFACTORING:
+ o CLEANUP: Package no longer utilizes ':::'.
-Version: 0.15.0 [2011-10-20]
-o Added support for specifying priorly known segments, such as chromosome
- arms and centromeres, in segmentByCBS() via argument 'knownSegments'.
-o CLEANUP: Dropped a stray debug output message in segmentByPairedPSCBS().
+Version: 0.36.0 [2013-08-15]
-Version: 0.14.3 [2011-10-17]
-o Added argument 'asMissing' to dropRegions() for AbstractCBS.
+NEW FEATURES:
+ o Made extractMinorMajorCNs() for PairedPSCBS acknowledge additional fields
+ related to (C1,C2).
-Version: 0.14.2 [2011-10-16]
-o Implemented extractCNs() for CBS and PairedPSCBS.
-o Added extractTotalCNs() for CBS.
+Version: 0.35.6 [2013-08-01]
-Version: 0.14.1 [2011-10-14]
-o Added implementation of extractRegions() for AbstractCBS, which
- utilizes extractSegments().
-o Added abstract extractSegments() and extractSegment() for AbstractCBS.
-o Now extractTCNAndDHs() for PairedPSCBS passes '...' to getSegments().
+CODE REFACTORING:
+ o Updated the vignettes to utilize the new R.rsp features.
-Version: 0.14.0 [2011-10-10]
-o CLEANUP: Harmonization of several method names.
-o CLEANUP: Internal restructuring of the source code files.
+Version: 0.35.5 [2013-07-19]
-Version: 0.13.5 [2011-10-10]
-o Added dropChangePoint() for AbstractCBS, which is just a
- "name wrapper" for mergeTwoSegments().
-o Added dropRegion() and dropRegions() for AbstractPSCBS, where
- the former is a wrapper for the latter dropRegions().
-o Added updateMeans() and mergeTwoSegments() for CBS in addition
- already available PairedPSCBS versions.
-o Relabeled column 'id' to 'sampleName' returned by getSegments().
-o ROBUSTNESS: Now using getSegments() everywhere possible.
-o BUG FIX: For so called "splitter" rows, not all columns returned
- by getSegments() of CBS were missing values.
-o BUG FIX: The object returned by as.CBS() of DNAcopy did not have the
- correct class hierarchy.
+NEW FEATURES:
+ o ROBUSTNESS: Added a sanity check on the estimates of (tauA, tauB) when they
+ are estimated from data in segmentByNonPairedPSCBS().
-Version: 0.13.4 [2011-10-08]
-o Added all.equal() for AbstractCBS, which does not compare attributes.
-o Now internal getChromosomeRanges() of CBS returns a data.frame
- instead of a matrix, and first column is now 'chromosome'.
-o Added optional argument 'regions' to getCallStatistics() of CBS
- in order to calculate call statistics on subsets of chromosomes,
- e.g. chromosome arms.
-o Added drawChromosomes() for CBS.
-o Added getCallStatisticsByArms(), callArms() and highlightArmCalls()
- for CBS objects.
+Version: 0.35.4 [2013-07-11]
-Version: 0.13.3 [2011-10-03]
-o GENERALIZATION: Now segmentByCBS() and segmentByPairedPSCBS()
- also accepts a data.frame of locus-level data with column names
- matching the locus-level arguments accepted by the corresponding
- method.
-o GENERALIZATION: Now all segmentation result classes (CBS and PSCBS)
- inherits from the AbstractCBS class, which provides methods such
- as getSampleName(), getChromosomes() and getSegments().
-o DOCUMENTATION: Added lots of more help pages.
-o CLEANUP: Dropped empty callSegments() for PairedPSCBS.
+CODE REFACTORING:
+ o Updated the Makefile for the vignettes and added .Rinstignore such that
+ auxiliary (bib and bst) LaTeX files are not installed but part of the build
+ so they are available to R CMD check, which is recently needed by R devel.
-Version: 0.13.2 [2011-09-30]
-o GENERALIZATION: Now drawLevels() for PairedPSCBS allows for drawing
- segmentation results in 'betaT' space.
-o BUG FIX: plotTracks2(..., panels="dh") gave an error due to a
- forgotten assignment.
+ o Bumped package dependencies.
-Version: 0.13.1 [2011-09-06]
-o Added formal class CBS, which holds the segmentation results
- returned by segmentByCBS(). Several methods are available for
- CBS objects, e.g. nbrOfLoci(), nbrOfSegments(), nbrOfChromosomes(),
- getChromosomes(), estimateStandardDeviation() etc.
-o Now segmentByCBS() always returns a CBS object. To coerce to a
- DNAcopy object (as defined in the DNAcopy class) use as.DNAcopy().
-o Added coerce methods as.DNAcopy() for CBS objects and as.CBS()
- for DNAcopy objects.
+Version: 0.35.3 [2013-05-25]
+CODE REFACTORING:
-Version: 0.13.0 [2011-09-01]
-o GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.
-o BUG FIX: Internal methods plotTracksManyChromosomes() and
- tileChromosomes() for CBS did not work at all and therefore
- neither plotTracks() for CBS with more than one chromosome.
-o Added append() for CBS objects.
+ o Minor speedup by replacing all rm(x) with x <- NULL, cf. R-devel thread
+ 'Assigning NULL to large variables is much faster than rm() - any reason why
+ I should still use rm()?' on May 25, 2013.
-Version: 0.12.2 [2011-08-27]
-o CLEANUP: Now R CMD check is no longer giving a note that the
- package loads package 'DNAcopy' in .onAttach().
+Version: 0.35.2 [2013-05-20]
+DOCUMENTATION:
-Version: 0.12.1 [2011-08-08]
-o BUG FIX: If dropSegmentationOutliers() would drop an outlier next to
- a change point, such that the total copy-number signal becomes NA,
- then the sanity checks that TCN segments always overlaps DH segments
- would fail. Now the sanity checks are aware of this special case.
- These sanity checks were moved from bootstrapTCNandDHByRegion() to
- segmentByPairedPSCBS(). Thanks Christine To at University of Toronto
- for reporting on this.
+ o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
-Version: 0.12.0 [2011-07-23]
-o Added a namespace to the package, which will be more or less
- a requirement in the next major release of R.
-o BUG FIX: Recently R devel automatically adds a namespace to
- a package, if missing. This caused some of the PSCBS examples
- to throw an exception related to incorrect dispatching of cat().
+Version: 0.35.1 [2013-05-07]
+NEW FEATURES:
-Version: 0.11.7 [2011-07-15]
-o DOCUMENTATION: Added a section to help("segmentByPairedPSCBS") on
- the importance of doing a whole-genome PSCBS segmentations if
- calling AB and LOH states afterward.
-o DOCUMENTATION: Made it more clear in help("segmentByPairedPSCBS")
- that arguments 'betaT', 'betaN' and 'muN' may contain NAs for
- non-polymorphic loci.
+ o Now estimateDeltaCN() for PairedPSCBS adjust for the ploidy if set.
+ o Added ploidy() and ploidy()<- for AbstractCBS.
-Version: 0.11.6 [2011-07-14]
-o BUG FIX/ROBUSTNESS: In some cases, the segmentation table would
- contain column names with incorrect capitalization, e.g. "tcnnbrOfLoci"
- instead of "tcnNbrOfLoci". This would cause several downstream
- methods to give an error. The reason for this is that the Hmisc
- package, if loaded after R.utils, overrides capitalize() in R.utils
- with another (buggy?) capitalize() function. To avoid this, we
- now everywhere specify explicitly that we want the one in R.utils.
- Thanks Christine To at University of Toronto for reporting on this.
+ o Now tileChromosomes() no longer gives warnings on "max(i): no non-missing
+ arguments to max; returning -Inf".
-Version: 0.11.5 [2011-07-10]
-o ROBUSTNESS: Fixed partial argument matchings in arrowsC1C2() and
- arrowsDeltaC1C2() for PairedPSCBS.
-o BUG FIX: tileChromosomes() for PairedPSCBS was still assuming the
- old naming convention of column names. This caused plotTracks()
- to throw an exception when plotting multiple chromosomes.
+Version: 0.35.0 [2013-04-23]
+NEW FEATURES:
-Version: 0.11.4 [2011-07-07]
-o GENERALIZATION: Now the internal estimator function that
- estimateDeltaLOH() uses returns -Inf if all segments are called AB,
- instead of throwing an exception. This will in turn make callLOH()
- call all segments to be non-LOH.
-o DOCUMENTATION: Removed obsolete references to the R-forge repository.
-o BUG FIX: Consecutive calls to callAB(..., force=TRUE) would append
- additional 'abCall' columns to the segmentation table instead of
- replacing existing calls.
+ o SPEEDUP: Now bootstrapTCNandDHByRegion() for PairedPSCBS always estimates
+ the default quantiles in addition to any requested ones.
+ o SPEEDUP: Made bootstrapTCNandDHByRegion() much faster by adding
+ use.names = FALSE to two internal unlist() statements.
-Version: 0.11.3 [2011-07-06]
-o ROBUSTNESS: Added a sanity check to estimateDeltaLOHByMinC1AtNonAB() for
- PairedPSCBS object. The test asserts that there exist segments that are
- not in allelic balance, which are needed in order to estimate DeltaLOH.
-o DOCUMENTATION: The description of argument 'chromosome' for
- segmentByPairedPSCBS() did not describe how to segment multiple
- chromosomes in one call.
+BUG FIXES:
+ o updateMeans() for PairedPSCBS and NonPairedPSCBS could include a signal from
+ a neighboring segment when averaging, iff that signal was located at the
+ exact locus of the change point. Thanks Ingrid L�nnstedt (WEHI) for
+ reporting on this.
-Version: 0.11.2 [2011-07-05]
-o BUG FIX: Output fields 'tcnNbrOfSNPs' and 'tcnNbrOfHets' were
- mistakenly labeled as 'tcnNbrOr...'. Thanks Christine Ho at
- UC Berkeley for reporting on this.
+Version: 0.34.9 [2013-04-22]
-Version: 0.11.1 [2011-06-28]
-o DOCUMENTATION: Clarified that argument 'CT' should be tumor copy
- number ratios relative to the normal.
-o DOCUMENTATION: Added Rd help for as.data.frame() of PairedPSCBS.
+BUG FIXES:
+ o updateMeans() would not always preserve the originally specified
+ segment-mean level estimator, if different from a (sample) mean estimator,
+ e.g. avgDH = "median". This could result in for instance callAB() failing
+ on internal sanity checks.
-Version: 0.11.0 [2011-06-14]
-o Renamed all column names of returned data frames such that
- they follow the camelCase naming conventions in addition
- to be somewhat shorter too.
-o GENERALIZATION: Added argument 'columnNamesFlavor' to segmentByCBS().
+ o Segment levels drawn by plotTracks() would have incorrect genomic locations
+ for chromosome 2 and beyond. This bug was introduced in v0.34.7.
+CODE REFACTORING:
-Version: 0.10.2 [2011-06-07]
-o CLEANUP: Cleaned up the example():s.
-o Added more biocViews categories to DESCRIPTION
+ o Utilizing new startupMessage() of R.oo.
-Version: 0.10.1 [2011-05-31]
-o GENERALIZATION: The package can now be *installed* without the
- DNAcopy package being installed. If package is loaded without
- DNAcopy installed, an informative message will explain how to
- install it.
-o Added installDNAcopy(), which will install DNAcopy from Bioconductor.
-o ROBUSTNESS: Now all DNAcopy functions are called as DNAcopy::nnn().
+Version: 0.34.8 [2013-04-20]
+DEPRECATED AND DEFUNCT:
-Version: 0.10.0 [2011-05-29]
-o Renamed all arguments, variables, and functions referring to 'tau' to
- refer to 'delta' reflecting the notation of the Paired PSCBS paper.
-o Renamed options, example code and help pages to reflect new package name.
-o Updated references in help pages.
-o Now the paired PSCBS is formally referred to as 'Paired PSCBS'.
-o Renamed package to PSCBS (from 'psCBS').
+ o Removed previously deprecated methods for AbstractCBS.
-Version: 0.9.54 [2011-04-27]
-o Added argument 'maxC' to estimateTauLOHByMinC1ForNonAB().
+Version: 0.34.7 [2013-04-18]
+NEW FEATURES:
-Version: 0.9.53 [2011-04-14]
-o Added argument 'max' to estimateTauAB() and estimateTauLOH().
+ o Added more arguments to plotTracks().
+ o Now drawLevels() and drawConfidenceBands() for CBS and PairedPSCBS also
+ works for multiple chromosomes.
-Version: 0.9.52 [2011-04-14]
-o BUG FIX: Argument 'minSize' of callAB() and callLOH() had no effect.
+BUG FIXES:
+ o One of the system tests for segmentByPairedPSCBS() failed in the case when
+ the data was downsampled (in order to meet the CRAN requirements). The
+ workaround is to use a fix 'deltaAB' parameter in that case.
-Version: 0.9.51 [2011-04-12]
-o Added argument 'minSize' to callAB() and callLOH() for PairedPSCBS.
-o Now the a conflicting call in callLOH()/callAB() with
- argument xorCalls=TRUE is set to NA to contrast it from
- a FALSE call.
+ o Internal calcStatsForCopyNeutralABs() would give an error if there was
+ exactly two AB segments.
-Version: 0.9.50 [2011-04-12]
-o Added argument 'xorCalls' to callLOH() and callAB() for
- PairedPSCBS. When TRUE (the default), a segment that
- is already called AB will never be called LOH, and vice versa.
+Version: 0.34.6 [2013-04-11]
+BUG FIXES:
-Version: 0.9.49 [2011-04-11]
-o Updated estimateTauABBySmallDH() for PairedPSCBS to use a
- "symmetric" quantile estimator.
-o Added argument 'midpoint' to estimateTauLOHByMinC1AtNonAB().
-o BUG FIX: The recent callLOH() would not store the LOH calls.
+ o plotTracks(fit, callLoci = TRUE) would color loci incorrectly if more than
+ one chromosome are plotted.
-Version: 0.9.48 [2011-04-10]
-o Added callLOH() for PairedPSCBS, which in turn calls
- auxiliary methods.
-o Added estimateTauLOH() for PairedPSCBS, which in turn calls
- axillary methods.
-o Now callAB(..., force=FALSE) skips the caller if
- allelic-balance calls already exist.
-o DOCUMENTATION: Update the example for segmentByPairedPSCBS
- to reflect the restructured AB and LOH callers.
+Version: 0.34.5 [2013-04-09]
+NEW FEATURES:
-Version: 0.9.47 [2011-04-08]
-o Added estimateTauABBySmallDH()
-o Added internal weightedQuantile().
-o DOCUMENTATION: Added help pages for more methods.
-o CLEANUP: Started to restructure the source code files.
+ o Now callROH() gives an informative error if called on a NonPairedPSCBS
+ object.
-Version: 0.9.46 [2011-04-08]
-o BUG FIX: postsegmentTCN() for PairedPSCBS could generate an invalid
- 'tcnSegRows' matrix, where the indices for two consecutive segments
- would overlap, which is invalid. This was caught with real data,
- but it seems to have required a very rare combination of data in
- order for it to occur.
+Version: 0.34.4 [2013-04-05]
+NEW FEATURES:
-Version: 0.9.45 [2011-04-05]
-o BUG FIX: estimateHighDHQuantileAtAB() for PairedPSCBS would throw
- an error on an undefined 'trim' if verbose output was used.
+ o Added more end-user control to plotTracks().
-Version: 0.9.44 [2011-02-18]
-o Added estimateHighDHQuantileAtAB() for PairedPSCBS.
+Version: 0.34.3 [2013-04-04]
+CODE REFACTORING:
-Version: 0.9.43 [2011-02-06]
-o BUG FIX: plotTracks2() queried non-existing argument 'tracks'.
+ o Now package builds with both R.rsp (< 0.9.1) and R.rsp (>= 0.9.1).
-Version: 0.9.42 [2011-02-03]
-o Added estimateKappa() for estimating the normal contamination.
+Version: 0.34.2 [2013-03-28]
+NEW FEATURES:
-Version: 0.9.41 [2011-02-02]
-o Updated default for 'tauAB' of callABandHighAI() and callABandLowC1()
- to be estimated from data using estimateTauAB().
-o Added argument 'tauTCN' to estimateTauAB().
+ o Now callGainNeutralLoss(), utilizes callCopyNeutral() by default.
-Version: 0.9.40 [2011-01-27]
-o Added argument 'flavor' to estimateTauAB() for estimating the
- AB threshold using alternative methods.
+Version: 0.34.1 [2013-03-21]
+NEW FEATURES:
-Version: 0.9.39 [2011-01-19]
-o Added trial version of new plotTracks2(), which will later replace
- plotTracks(). Currently it only works for single chromosomes.
-o Added support functions, e.g. updateMeans().
+ o Updated the report generator and its RSP templates.
+DOCUMENTATION:
-Version: 0.9.38 [2011-01-18]
-o DOCUMENTATION: Documented more plotTracks() arguments for PairedPSCBS.
-o BUG FIX: Now plotTracks(..., add=TRUE) for PairedPSCBS plots to
- the current figure/panel.
-o Now plotTracks(..., add=FALSE) for PairedPSCBS only sets up subplots
- if argument 'tracks' specifies more than one panel.
-o Added arguments 'changepoints' and 'col' to plotTracks() for PairedPSCBS.
+ o Clarified in the PSCBS vignette that the NTCN caller is under development,
+ experimental.
+CODE REFACTORING:
-Version: 0.9.37 [2011-01-18]
-o BUG FIX: 'tcnSegRows' and 'dhSegRows' where not updated by
- extractByRegions() for PairedPSCBS.
+ o SPEEDUP: Made dropChangePoints() faster by only updating the segment
+ statistics/means at the very end.
-Version: 0.9.36 [2011-01-14]
-o Added estimateTauAB() for estimating the tauAB tuning parameter
- when calling segments in allelic balance. Updated
- example(segmentByPairedPSCBS) to illustrate how to use it.
-o Added extractByRegions() for PairedPSCBS.
+Version: 0.34.0 [2013-03-19]
+NEW FEATURES:
-Version: 0.9.35 [2011-01-12]
-o Now postsegmentTCN(..., force=TRUE) for PairedPSCBS also updates
- the TCN estimates even for segments where the DH segmentation did
- not find any additional change points.
+ o CALLING: Defined a formal hypothesis test for how segments are called copy-
+ neutral in TCN (NTCN), with the null hypothesis being that a segment is
+ NTCN. In order for a segment to not be NTCN, its confidence interval has to
+ be completely outside the null region. This changed how
+ callCopyNeutralByTCNofAB() for PairedPSCBS calls segments; it is now a bit
+ more conservative in rejecting NTCN.
-Version: 0.9.34 [2010-12-09]
-o BUG FIX: When there were multiple chromosomes processed by
- segmentByPairedPSCBS(), then the returned data object would
- contain 'betaT' identical to 'betaTN'.
+Version: 0.33.4 [2013-03-19]
+NEW FEATURES:
-Version: 0.9.33 [2010-12-07]
-o Added callLowC1ByC1() and callABandLowC1().
+ o ROBUSTNESS: Now calcStatsForCopyNeutralABs() for PairedPSCBS does a better
+ job in identifying the TCN mode of the AB segments.
+ o Added argument 'flavor' to findNeutralCopyNumberState() specifying how to
+ identify the main mode of the AB segments.
-Version: 0.9.32 [2010-12-03]
-o BUG FIX: In rare cases the bootstrap sanity checks can indeed produce
- an invalid 'range', more precisely where (range[,2] >= range[,1]) is
- not true. This can happen if there is no variation in the bootstrap
- estimates. Because of this we allow for some tolerance.
+ o VISUALIZATION: Now plotTracks() for PairedPSCBS displays thresholds for
+ calling AB, LOH and and NTCN.
-Version: 0.9.31 [2010-12-02]
-o Added option "psCBS/sanityChecks/tolerance" for specifying the
- tolerance of some internal sanity checks.
+Version: 0.33.3 [2013-03-12]
+DOCUMENTATION:
-Version: 0.9.30 [2010-12-01]
-o Rewrote all code dealing with the identification of loci belong
- to segments. The code is now utilizing the 'segRows' element
- returned by DNAcopy::segment(). Lots of the code was rewritten
- and therefore completely new bugs may have been introduced.
+ o Documented 'tauA' and 'tauB' in the help for segmentByNonPairedPSCBS().
-Version: 0.9.25 [2010-11-30]
-o BUG FIX: Argument 'flavor' of segmentByPairedPSCBS() would be ignored
- if multiple chromosomes were segmented.
-o BUG FIX: extractByChromosome() for PSCBS would call it self instead
- of extractByChromosomes().
+Version: 0.33.2 [2013-03-09]
+NEW FEATURES:
-Version: 0.9.24 [2010-11-28]
-o BUG FIX: postsegmentTCN() did not handle loci with the same positions
- and that are split in two different segments. It also did not exclude
- loci with missing values.
+ o Added getLocusData() for PairedPSCBS and NonPairedPSCBS.
+DOCUMENTATION:
-Version: 0.9.23 [2010-11-28]
-o BUG FIX: The algorithm in segmentByCBS() that infers which loci (of
- the ones share the same genomic positions) that should be exclude
- from each segment did not take missing signals into account.
-o BUG FIX: Iff argument 'chromosome' to segmentByPairedPSCBS() was of
- length greater than one and specified exactly one unique chromosome,
- then exception "Number of elements in argument 'chromosome' should
- be exactly 8712 not 86209 value(s)" would be thrown.
+ o Updated the vignettes and the report templates to utilize the new ggplot2
+ themes - ggplot2 no longer gives a warning on using deprecated functions.
+ o Now report() for AbstractCBS also includes files listed in the optional file
+ '.install_extras' of the source RSP template directory. The same filename
+ is used by 'R CMD build/check' for including additional source files needed
+ to build the vignettes.
-Version: 0.9.22 [2010-11-27]
-o BUG FIX: bootstrapTCNandDHByRegion() would incorrectly include
- non-polymorphic loci in the set of homozygous SNPs during resampling.
-o BUG FIX: segmentByPairedPSCBS() would not accept missing values in
- argument 'chromosome'.
+CODE REFACTORING:
+
+ o Added an Authors at R field to the DESCRIPTION.
+
+
+Version: 0.33.1 [2013-03-07]
+
+DOCUMENTATION:
+
+ o Preparing package vignettes for the upcoming R 3.0.0 support for non-Sweave
+ vignettes.
+
+SOFTWARE QUALITY:
+
+ o Relaxed the internal precision tests of testROH(). This was done in
+ response to the CRAN farm lowering its precision on some hosts.
+
+
+Version: 0.33.0 [2013-03-05]
+
+NEW FEATURES:
+
+ o Added argument 'typeOfWeights' to estimateKappaByC1Density() for
+ PairedPSCBS, and hence indirectly to estimateKappa(). The default is
+ typeOfWeights = "dhNbrOfLoci", which may give too much overall weight to
+ very long segments causing the estimator to fail when there are only a few
+ number of "C1 = 0" segments. An alternative is to use
+ typeOfWeights = "sqrt(dhNbrOfLoci)".
+
+
+Version: 0.32.6 [2013-03-04]
+
+DOCUMENTATION:
+
+ o Updated the help usage section for all static methods.
+
+
+Version: 0.32.5 [2013-02-09]
+
+BUG FIXES:
+
+ o bootstrapTCNandDHByRegion() for PairedPSCBS did not bootstrap from all
+ available loci when calculating total CNs statistics, iff the segment had
+ been called run-of-homozygosity (ROH). Internal validation tests caught
+ this. Thanks to Oscar Rueda at the Cancer Research UK Cambridge Institute
+ for reporting on this.
+
+CODE REFACTORING:
+
+ o Added a VignetteBuilder field to DESCRIPTION.
+
+
+Version: 0.32.4 [2013-02-07]
+
+NEW FEATURES:
+
+ o Improved some verbose outputs of bootstrapTCNandDHByRegion().
+
+
+Version: 0.32.3 [2013-02-05]
+
+NEW FEATURES:
+
+ o Now pruneByHClust() drops any existing segment calls and quantile mean-level
+ estimates.
+
+
+Version: 0.32.2 [2013-02-01]
+
+NEW FEATURES:
+
+ o Added resetSegments() for AbstractCBS, which drops extra segments columns
+ (e.g. bootstrap statistics and calls) except those obtained from the segment
+ algorithm.
+
+DOCUMENTATION:
+
+ o Added a paragraph on avgDH = "median" to the PSCBS vignette's 'Experimental'
+ section.
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Now aroma.light is explicitly required in cases where it is
+ needed.
+
+
+Version: 0.32.1 [2013-02-01]
+
+BUG FIXES:
+
+ o segmentByPairedPSCBS(..., avgDH = "median") only worked for single-
+ chromosome data. Same for avgTCN = "median". Thanks Ritu Roy at UCSF for
+ reporting on this.
+
+
+Version: 0.32.0 [2013-01-16]
+
+NEW FEATURES:
+
+ o Added arguments 'avgTCN' and 'avgDH' to segmentByPairedPSCBS().
+
+ o Now updateMeans() and updateMeansTogether() methods can estimate the mean
+ levels either by the sample mean or the median.
+
+
+Version: 0.31.0 [2013-01-05]
+
+CODE REFACTORING:
+
+ o CLEANUP: Now packages R.methodsS3 and R.oo are only imported.
+
+ o CLEANUP: Package no longer explicitly imports digest.
+
+
+Version: 0.30.0 [2012-11-05]
+
+NEW FEATURES:
+
+ o GENERALIZATION: Now bootstrapTCNandDHByRegion() works for more "flavors",
+ e.g the default ('tcn') used by segmentByNonPairedPSCBS().
+
+
+Version: 0.29.9 [2012-11-05]
+
+DOCUMENTATION:
+
+ o FIX: example(segmentByNonPairedPSCBS) was for the paired case.
+
+CODE REFACTORING:
+
+ o CRAN POLICY: Further speed up of examples such that they run faster with
+ 'R CMD check'.
+
+
+Version: 0.29.8 [2012-11-04]
+
+CODE REFACTORING:
+
+ o CLEANUP: Replaced all whichVector() with which(), because the latter is now
+ the fastest again.
+
+
+Version: 0.29.7 [2012-11-03]
+
+CODE REFACTORING:
+
+ o Updated deprecated ggplot2 functions in the RSP reports.
+
+
+Version: 0.29.6 [2012-11-01]
+
+CODE REFACTORING:
+
+ o Bumped package dependencies.
+
+ o CRAN POLICY: Made the examples run faster for 'R CMD check'.
+
+
+Version: 0.29.5 [2012-10-16]
+
+BUG FIXES:
+
+ o ROBUSTNESS: 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: 0.29.4 [2012-09-23]
+
+NEW FEATURES:
+
+ o Now plotTracks() [and plotTracksManyChromosomes()] draws segment levels such
+ that it is easier to see them even when they are overlapping.
+
+
+Version: 0.29.3 [2012-09-21]
+
+NEW FEATURES:
+
+ o SPEEDUP: By default bootstrapTCNandDHByRegion() for PairedPSCBS no longer do
+ sanity checks within the bootstrap loop. This significantly speed up the
+ method. To run checks, use argument .debug = TRUE. In addition, the
+ callNnn() methods that need to call this method, does it by decreasing the
+ amount of verbose output substantially, which in turn speeds up the process
+ a fair bit.
+
+ o Now getSegments(..., splitters = TRUE) for CBS and PSCBS inserts NA rows
+ wherever there is a "gap" between segments. A "gap" is when two segments
+ are not connected (zero distance).
+
+ o ROBUSTNESS: Now append() for CBS and PSCBS drops column 'length' from
+ 'knownSegments', iff it exists.
+
+ o Now nbrOfChangePoints() for AbstractCBS calculates only change points of
+ connected neighboring segments.
+
+BUG FIXES:
+
+ o seqOfSegmentsByDP() for AbstractCBS would not handle empty segments, which
+ could occur if 'knownSegments' for instance included centromere gaps.
+
+ o segmentByCBS(... knownSegments) could return segments for chromosome 0 even
+ though it did not exist in the input data.
+
+
+Version: 0.29.2 [2012-09-18]
+
+NEW FEATURES:
+
+ o REPORT: Now report() for AbstractCBS looks for the RSP template in
+ templates/, and as a backup in templates,PSCBS/. If the latter does not
+ exist, it is automatically created as a soft link to templates/ of the PSCBS
+ package. This allows anyone to create their own customized copy (in
+ templates/) of the default PSCBS RSP report.
+
+ o REPORT: Now report(fit, ..., rspTags) for AbstractCBS looks for the RSP
+ template named <className>(,<rspTags>),report.tex.rsp, where className is
+ class(fit)[1] and argument 'rspTags' is an optional comma-separated
+ character string/vector. This makes it possible to have different types of
+ report for the same class of objects.
+
+ o REPORT: Added argument 'force' to report() for AbstractCBS. This will copy
+ the RSP template files again, although they are already in reports/ output
+ directory.
+
+
+Version: 0.29.1 [2012-09-15]
+
+NEW FEATURES:
+
+ o Added argument 'dropMissingCT' to segmentByPairedPSCBS().
+
+
+Version: 0.29.0 [2012-09-14]
+
+NEW FEATURES:
+
+ o Added trial version of pruneByDP() for AbstractCBS.
+
+
+Version: 0.28.6 [2012-09-13]
+
+NEW FEATURES:
+
+ o Now tileChromosomes() also adjusts 'knownSegments'.
+
+ o Added argument 'dropGaps' to gapsToSegments().
+
+ o Updated all.equal() for AbstractCBS to compare locus-level data, segments,
+ and other fields.
+
+
+Version: 0.28.5 [2012-09-13]
+
+NEW FEATURES:
+
+ o SPEEDUP: Now segmentByCBS(..., undo = +Inf) returns much faster, which is
+ possible because there is no need to identify new change points.
+
+
+Version: 0.28.4 [2012-09-13]
+
+NEW FEATURES:
+
+ o CONSISTENCY FIX: Changed the behavior of extreme values of argument 'undo'
+ to segmentByCBS() such that 'undo = 0' (was 'undo = +Inf') now means that
+ it will not ask DNAcopy::segment() to undo the segmentation, and such that
+ 'undo = +Inf' means that no changepoints will be identified. The latter case
+ allows you to effectively skip the segmentation but still calculate all the
+ CBS statistics across a set of known segments via segmentByCBS(...,
+ undo = +Inf, knownSegments = knownSegments). Arguments 'undoTCN' and
+ 'undoDH' to segmentByPairedPSCBS() are adjusted analogously. Corresponding
+ system tests were added.
+
+
+Version: 0.28.3 [2012-08-30]
+
+CODE REFACTORING:
+
+ o Updated code and Rd cross reference to use the 'matrixStats' package for
+ weightedMedian(), which used to be in 'aroma.light'.
+
+
+Version: 0.28.2 [2012-08-20]
+
+BUG FIXES:
+
+ o segmentByNonPairedPSCBS() forgot to specify namespace aroma.light when
+ trying to call findPeaksAndValleys().
+
+
+Version: 0.28.1 [2012-08-15]
+
+DOCUMENTATION:
+
+ o Minor grammatical corrections of the Paired PSCBS vignette.
+
+
+Version: 0.28.0 [2012-07-22]
+
+NEW FEATURES:
+
+ o Added argument 'minLength' to gapsToSegments(). The default is no longer to
+ drop zero-length (minLength == -1L) segments, because if (and only if) such
+ a segment contains a locus, then segmentByNnn() will currently generate an
+ (internal) error.
+
+BUG FIXES:
+
+ o GENERALIZATION: Now segmentByPairedPSCBS() drops loci for which CT is
+ missing (regardless of betaT). For instance, in rare cases when the
+ reference (e.g. the normal) is missing, then it may be that CT is missing
+ while betaT is not.
+
+
+Version: 0.27.4 [2012-07-22]
+
+NEW FEATURES:
+
+ o Now verbose output of segmentByPairedPSCBS() specifies region ranges with
+ greater precision.
+
+
+Version: 0.27.3 [2012-07-10]
+
+DOCUMENTATION:
+
+ o Minor updates to the Paired PSCBS vignettes.
+
+CODE REFACTORING:
+
+ o CLEANUP: One redundancy tests relied on a non-critical function that will be
+ removed in R.utils 1.16.0 (now in R.devices 2.1.1).
+
+
+Version: 0.27.2 [2012-07-08]
+
+CODE REFACTORING:
+
+ o Updated package dependencies.
+
+
+Version: 0.27.1 [2012-07-02]
+
+NEW FEATURES:
+
+ o Now we refer to "copy neutral" segments as "neutral TCN" segments with
+ acronym 'NTCN'. The corresponding column in the segmentation results are
+ labeled correspondingly. The Paired PSCBS vignette was updated accordingly.
+
+
+Version: 0.27.0 [2012-06-24]
+
+DOCUMENTATION:
+
+ o Some grammar corrections of the 'Paired PSCBS' vignette.
+
+CODE REFACTORING:
+
+ o (An update that should be ignored)
+
+
+Version: 0.26.1 [2012-06-05]
+
+NEW FEATURES:
+
+ o Now segmentByCBS() for data frame:s does a better job identifying the CN
+ signals.
+
+
+Version: 0.26.0 [2012-06-03]
+
+NEW FEATURES:
+
+ o Now argument 'delta' for callCopyNeutralByTCNofAB() of PairedPSCBS is
+ calculated via estimateDeltaCN(), which estimates the width of the
+ acceptance regions, used for calling copy neutral states, to be a function
+ of the normal contamination.
+
+DOCUMENTATION:
+
+ o Added details to the Paired PSCBS vignette on how to call segments that are
+ copy neutral (typically diploid).
+
+
+Version: 0.25.3 [2012-06-03]
+
+BUG FIXES:
+
+ o all.equal(target, current) for CBS objects would give an error if either
+ 'target' or 'current' had zero segments.
+
+
+Version: 0.25.2 [2012-05-30]
+
+NEW FEATURES:
+
+ o Added writeSegments() for DNAcopy objects.
+
+BUG FIXES:
+
+ o as.CNA() for DNAcopy added incorrect chromosome splitters.
+
+ o as.CNA() for DNAcopy would ignore argument 'sample' and always return the
+ first sample.
+
+
+Version: 0.25.1 [2012-05-30]
+
+NEW FEATURES:
+
+ o Now callROH() records parameter 'deltaROH' in the results.
+
+DOCUMENTATION:
+
+ o Added details to the Paired PSCBS vignette on how to tune the various
+ callers.
+
+BUG FIXES:
+
+ o callLOH(..., force = TRUE) would append multiple 'lohCall' columns, if
+ called multiple times.
+
+
+Version: 0.25.0 [2012-04-20]
+
+NEW FEATURES:
+
+ o Added a trial (very much true) version of segmentByNonPairedPSCBS().
+
+
+Version: 0.24.0 [2012-04-20]
+
+NEW FEATURES:
+
+ o Now it is possible to skip the DH segmentation in Paired PSCBS, i.e.
+ segmentByPairedPSCBS(..., flavor = "tcn").
+
+
+Version: 0.23.2 [2012-04-20]
+
+BUG FIXES:
+
+ o segmentByPairedPSCBS() would throw "error in `$<-.data.frame
+ `(`*tmp*`, "rho" ..." if some loci had unknown genomic positions.
+
+
+Version: 0.23.1 [2012-04-20]
+
+NEW FEATURES:
+
+ o Added RSP report for CBS objects (adopted from ditto for PairedPSCBS).
+
+DOCUMENTATION:
+
+ o Updated the 'Paired PSCBS' vignette.
+
+
+Version: 0.23.0 [2012-03-20]
+
+DOCUMENTATION:
+
+ o Added a package vignette.
+
+
+Version: 0.22.2 [2012-02-29]
+
+BUG FIXES:
+
+ o plotTracks(..., add = TRUE) for PairedPSCBS would add TCNs when BAFs and DHs
+ were intended.
+
+
+Version: 0.22.1 [2012-02-28]
+
+ o Updated package dependencies to R.rsp (>= 0.7.3) so that report() for
+ PairedPSCBS no longer require non-public packages.
+
+NEW FEATURES:
+
+ o Now it is possible to turn off usage of the alpha channel in plots generated
+ by report(), which can be handy on systems where the default PNG device does
+ not support the alpha channel. Example:
+ setOption("PSCBS::report/useAlphaChannel", FALSE).
+
+
+Version: 0.22.0 [2012-02-27]
+
+NEW FEATURES:
+
+ o Added report() for PairedPSCBS.
+
+
+Version: 0.21.0 [2012-02-27]
+
+NEW FEATURES:
+
+ o Added argument 'fields' to getLocusData() for PairedPSCBS.
+
+ o Added renameChromosomes() to AbstractCBS.
+
+
+Version: 0.20.0 [2012-02-26]
+
+NEW FEATURES:
+
+ o Added alpha version of callGainNeutralLoss() for PairedPSCBS, which
+ certainly will be updated in the future. This caller is tested by the
+ system tests.
+
+ o Added dropChangePoints() for AbstractCBS.
+
+BUG FIXES:
+
+ o extractSegments() for PairedPSCBS would return incorrect row indices, more
+ precisely, overlapping data chunks.
+
+ o bootstrapTCNandDHByRegion() for PairedPSCBS would resample from a subset of
+ the intended TCNs, iff the DH mean was non-finite while there were still
+ heterozygous SNPs. This introduced a bias in the estimates, which was
+ neglectable for large segments, but for very small segments (a few loci) it
+ could be relatively large.
+
+SOFTWARE QUALITY:
+
+ o ROBUSTNESS: Added more sanity checks validating the correctness of what is
+ returned by extractSegments() for CBS and PairedPSCBS.
+
+CODE REFACTORING:
+
+ o Added some internal utility functions for PairedPSCBS taken from the
+ aroma.cn package. Some of these may become public later, but for they
+ should be considered internal.
+
+
+Version: 0.19.8 [2012-02-23]
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Package now explicitly depends on 'utils'.
+
+
+Version: 0.19.7 [2012-02-22]
+
+BUG FIXES:
+
+ o findLargeGaps() did not handle missing values for argument 'chromosome'.
+
+ o segmentByCBS(..., knownSegments = knownSegments) would incorrectly throw a
+ sanity-check exception if 'knownSegments' contains a segment with 'start'
+ and 'stop' positions being equal.
+
+ o Argument 'calls' of plotTracks() for PairedPSCBS was ignored if more than
+ one chromosome was plotted.
+
+
+Version: 0.19.6 [2012-01-24]
+
+NEW FEATURES:
+
+ o ROBUSTNESS: Now getCallStatistics() for CBS asserts that calls have been
+ made. If not, an exception is thrown.
+
+
+Version: 0.19.5 [2012-01-21]
+
+DOCUMENTATION:
+
+ o Added details to the help of callLOH() and callAB() on the difference
+ between (AB,LOH) = (TRUE,FALSE) and (AB,LOH) = (TRUE,NA).
+
+ o Corrected some of verbose messages of estimateDeltaLOHByMinC1ForNonAB() for
+ PairedPSCBS objects.
+
+
+Version: 0.19.4 [2012-01-10]
+
+CODE REFACTORING:
+
+ o Now example(segmentByPairedPSCBS) and the system tests that are run by
+ 'R CMD check' are tuned to (by default) run much faster by segmenting using
+ fewer data points and bootstrapping using fewer samples. This update was
+ done to meet the new CRAN policy. By setting environment variable
+ _R_CHECK_FULL_ to '1' the full data set is used instead.
+
+
+Version: 0.19.3 [2012-01-09]
+
+NEW FEATURES:
+
+ o ROBUSTNESS: Now extractSegments() for PairedPSCBS gives an informative error
+ message that it is not supported if CNs were segmented using flavor "tcn,dh".
+
+BUG FIXES:
+
+ o postsegmentTCN() for PairedPSCBS could generate an invalid 'tcnSegRows'
+ matrix, where the indices for two consecutive segments would overlap, which
+ is invalid. Thanks to Minya Pu for reporting on failed sanity check related
+ to this.
+
+
+Version: 0.19.2 [2011-12-29]
+
+ o ROBUSTNESS: Explicitly added 'digest' to the list of suggested packages.
+
+
+Version: 0.19.1 [2011-12-13]
+
+NEW FEATURES:
+
+ o Added support for callGainsAndLosses(..., method = "ucsf-dmad") of CBS
+ objects.
+
+
+Version: 0.19.0 [2011-12-12]
+
+NEW FEATURES:
+
+ o Added optional argument 'indices' to getLocusData() to be able to retrieve
+ the locus-level data as indexed by input data.
+
+BUG FIXES:
+
+ o gapsToSegments() gave invalid segments for chromosomes with more than one
+ gap. Now gapsToSegments() validates argument 'gaps' and asserts that it
+ returns non-overlapping segments.
+
+DOCUMENTATION:
+
+ o Clarified in help("segmentByCBS") how missing values are dealt with.
+
+
+Version: 0.18.2 [2011-12-07]
+
+NEW FEATURES:
+
+ o Now plotTracks() for CBS always returns an invisible object.
+
+BUG FIXES:
+
+ o pruneBySdUndo() for CBS did not work with more than one array.
+
+
+Version: 0.18.1 [2011-12-03]
+
+NEW FEATURES:
+
+ o Added drawChangePoints() for AbstractCBS.
+
+ o Now pruneByHClust() for AbstractCBS updates the segment means.
+
+ o Added writeSegments() for PSCBS object.
+
+ o Now print() for AbstractCBS returns getSegments(..., simplify = TRUE).
+
+ o Added argument 'simplify' to getSegments().
+
+ o Added arguments 'name', 'tags' and 'exts' to writeSegments() and
+ writeLocusData() and dropped 'filename'.
+
+
+Version: 0.18.0 [2011-11-28]
+
+NEW FEATURES:
+
+ o Added pruneByHClust() for AbstractCBS, with implementation for CBS and
+ PairedPSCBS.
+
+ o extractCNs() for CBS would not return a matrix but a data.frame.
+
+BUG FIXES:
+
+ o extractTotalCNs() for CBS would give an error.
+
+
+Version: 0.17.4 [2011-11-26]
+
+NEW FEATURES:
+
+ o Added argument 'updateMeans = TRUE' to callROH() for PairedPSCBS.
+
+ o Now bootstrapTCNandDHByRegion() for PairedPSCBS preserves NAs for DH and
+ (C1,C2) quantiles, if the DH mean level is NA, which can happen when a
+ segment is called ROH. This also makes sure that a segment called ROH will
+ not be called AB.
+
+ o An internal sanity check of bootstrapTCNandDHByRegion() for PairedPSCBS
+ would give an error if DH mean levels had been set to NA for segments called
+ ROH.
+
+
+Version: 0.17.3 [2011-11-24]
+
+NEW FEATURES:
+
+ o Added callSegmentationOutliers() and dropSegmentationOutliers() for data
+ frames.
+
+ o CLEANUP: Renamed field 'position' of the example data to 'x'. This helps us
+ clean up some of the examples.
+
+BUG FIXES:
+
+ o bootstrapTCNandDHByRegion() for PairedPSCBS would give an error, if a
+ segment did not have any TCN signals, which can occur when known segments
+ are specified for Paired PSCBS.
+
+
+Version: 0.17.2 [2011-11-22]
+
+NEW FEATURES:
+
+ o Added findLargeGaps() and gapsToSegments().
+
+
+Version: 0.17.1 [2011-11-21]
+
+BUG FIXES:
+
+ o The internal sanity check of testROH() on weights was slightly too
+ conservative (required to high precision) when it came to asserting that the
+ sum of the weights equals one.
+
+ o resegment() for PairedPSCBS called segmentByCBS() instead of
+ segmentByPairedPSCBS().
+
+
+Version: 0.17.0 [2011-11-19]
+
+NEW FEATURES:
+
+ o Now it is possible to run Paired PSCBS (without TumorBoost) when only
+ genotypes but not BAFs are available for the matched normal.
+
+
+Version: 0.16.3 [2011-11-17]
+
+NEW FEATURES:
+
+ o Added resegment() for CBS and PairedPSCBS for easy resegmentation.
+
+ o Adjusted segmentByCBS() such that it can handle 'knownSegments' with
+ chromosome boundaries given as -Inf and +Inf.
+
+ o Now argument 'mar' for plotTracks() defaults to NULL.
+
+ o ROBUSTNESS: Added redundancy tests for segmentByCBS() and
+ segmentByPairedPSCBS() with argument 'knownSegments'.
+
+ o ROBUSTNESS: Now segmentByCBS() does more validation of 'knownSegments'.
+
+ o FIX: extractRegions() for AbstractCBS would also show verbose output.
+
+BUG FIXES:
+
+ o Now argument/parameter 'seed' is correctly preserved by segmentByCBS(). So
+ is 'tbn' for segmentByPairedPSCBS().
+
+ o segmentByPairedPSCBS() would give an error when trying to segment DH if the
+ TCN segment contains no data points, which could happen if 'knownSegments'
+ specifies an empty segment, e.g. centromere.
+
+ o extractSegments() for CBS would throw an error when there were multiple
+ chromosomes.
+
+
+Version: 0.16.2 [2011-11-16]
+
+NEW FEATURES:
+
+ o Now segmentByCBS(..., w) stores weights 'w', if given, in the locus-level
+ data table of the returned CBS object.
+
+ o Added pruneBySdUndo() for CBS, which does what undo.splits = "sdundo"' for
+ DNA::segment(), but on the already segmented results.
+
+ o Now updateMeans() uses locus-specific weights, iff available.
+
+ o Added updateBoundaries() for CBS to update (start,stop) per segment.
+
+ o CORRECTNESS: Now updateMeans() for CBS identifies loci via internal
+ 'segRows' field and no longer by locations of segment boundaries, which gave
+ slightly incorrect estimates for "tied" loci.
+
+
+Version: 0.16.1 [2011-11-15]
+
+NEW FEATURES:
+
+ o Now more segmentation parameters are stored in the CBS object.
+
+ o SPEEDUP: Now segmentByCBS() will use memoization to retrieve so called
+ "sequential boundaries for early stopping", iff any of the
+ DNAcopy::segment() arguments 'alpha', 'nperm' and 'eta' are specified.
+ See also DNAcopy::getbdry().
+
+ o Added method = "DNAcopy" to estimateStandardDeviation() for CBS, which
+ estimates the std. dev. using DNAcopy:::trimmed.variance().
+
+BUG FIXES:
+
+ o extractSegments() for CBS would throw an error, because in most cases it
+ would created a corrupt internal 'segRows' field.
+
+
+Version: 0.16.0 [2011-11-12]
+
+NEW FEATURES:
+
+ o Added argument 'oma' and 'mar' to plotTracksManyChromosomes() for
+ PairedPSCBS for setting graphical parameters when 'add' == FALSE.
+
+ o Added callROH().
+
+ o Added arguments 'from' and 'adjustFor' to updateMeans().
+
+
+Version: 0.15.5 [2011-11-04]
+
+BUG FIXES:
+
+ o extractSegment() for AbstractCBS would give an error, because it called
+ itself instead of extractSegments().
+
+
+Version: 0.15.4 [2011-10-30]
+
+NEW FEATURES:
+
+ o Added save() and load() methods to AbstractCBS, which are wrappers for
+ saveObject() and loadObject() that assert the correct class structure.
+ Also, the load() method will automatically update the class hierarchy for
+ CBS and PairedPSCBS objects that were saved before adding class AbstractCBS.
+
+
+Version: 0.15.3 [2011-10-23]
+
+BUG FIXES:
+
+ o callAmplifications() for CBS generated an error, if more than one chromosome
+ were called.
+
+ o The length of a segment must be defined as 'end-start' and not 'end-start+1'
+ so that the the total length of all segments adds up correctly.
+
+ o highlightArmCalls() for CBS did not handle empty chromosomes.
+
+ o getCallStatisticsByArms() for CBS threw a error if argument 'genomeData' did
+ not contain exactly the same chromosomes as in the CBS object.
+
+
+Version: 0.15.2 [2011-10-21]
+
+NEW FEATURES:
+
+ o Added mergeThreeSegments() to AbstractCBS.
+
+BUG FIXES:
+
+ o Recent updates caused segmentByPairedPSCBS(data) not to work when 'data' is
+ a data frame.
+
+
+Version: 0.15.1 [2011-10-21]
+
+NEW FEATURES:
+
+ o By setting 'start' and 'end' to NAs in 'knownSegments' (chromosome must
+ still be specified), it is possible to insert an empty segment that
+ disconnects the two flanking segments, e.g. centromere and the two arms.
+
+
+Version: 0.15.0 [2011-10-20]
+
+NEW FEATURES:
+
+ o Added support for specifying priorly known segments, such as chromosome arms
+ and centromeres, in segmentByCBS() via argument 'knownSegments'.
+
+BUG FIXES:
+
+ o CLEANUP: Dropped a stray debug output message in segmentByPairedPSCBS().
+
+
+Version: 0.14.3 [2011-10-17]
+
+NEW FEATURES:
+
+ o Added argument 'asMissing' to dropRegions() for AbstractCBS.
+
+
+Version: 0.14.2 [2011-10-16]
+
+NEW FEATURES:
+
+ o Implemented extractCNs() for CBS and PairedPSCBS.
+
+ o Added extractTotalCNs() for CBS.
+
+
+Version: 0.14.1 [2011-10-14]
+
+NEW FEATURES:
+
+ o Added implementation of extractRegions() for AbstractCBS, which utilizes
+ extractSegments().
+
+ o Added abstract extractSegments() and extractSegment() for AbstractCBS.
+
+ o Now extractTCNAndDHs() for PairedPSCBS passes '...' to getSegments().
+
+
+Version: 0.14.0 [2011-10-10]
+
+CODE REFACTORING:
+
+ o CLEANUP: Harmonization of several method names.
+
+ o CLEANUP: Internal restructuring of the source code files.
+
+
+Version: 0.13.5 [2011-10-10]
+
+NEW FEATURES:
+
+ o Added dropChangePoint() for AbstractCBS, which is just a "name wrapper" for
+ mergeTwoSegments().
+
+ o Added dropRegion() and dropRegions() for AbstractPSCBS, where the former is
+ a wrapper for the latter dropRegions().
+
+ o Added updateMeans() and mergeTwoSegments() for CBS in addition already
+ available PairedPSCBS versions.
+
+ o Relabeled column 'id' to 'sampleName' returned by getSegments().
+
+BUG FIXES:
+
+ o For so called "splitter" rows, not all columns returned by getSegments() of
+ CBS were missing values.
+
+ o The object returned by as.CBS() of DNAcopy did not have the correct class
+ hierarchy.
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Now using getSegments() everywhere possible.
+
+
+Version: 0.13.4 [2011-10-08]
+
+NEW FEATURES:
+
+ o Added all.equal() for AbstractCBS, which does not compare attributes.
+
+ o Added optional argument 'regions' to getCallStatistics() of CBS in order to
+ calculate call statistics on subsets of chromosomes, e.g. chromosome arms.
+
+ o Added drawChromosomes() for CBS.
+
+ o Added getCallStatisticsByArms(), callArms() and highlightArmCalls() for CBS
+ objects.
+
+CODE REFACTORING:
+
+ o Now internal getChromosomeRanges() of CBS returns a data.frame instead of a
+ matrix, and first column is now 'chromosome'.
+
+
+Version: 0.13.3 [2011-10-03]
+
+NEW FEATURES:
+
+ o GENERALIZATION: Now segmentByCBS() and segmentByPairedPSCBS() also accepts a
+ data.frame of locus-level data with column names matching the locus-level
+ arguments accepted by the corresponding method.
+
+ o GENERALIZATION: Now all segmentation result classes (CBS and PSCBS) inherits
+ from the AbstractCBS class, which provides methods such as getSampleName(),
+ getChromosomes() and getSegments().
+
+DOCUMENTATION:
+
+ o Added lots of more help pages.
+
+CODE REFACTORING:
+
+ o CLEANUP: Dropped empty callSegments() for PairedPSCBS.
+
+
+Version: 0.13.2 [2011-09-30]
+
+NEW FEATURES:
+
+ o GENERALIZATION: Now drawLevels() for PairedPSCBS allows for drawing
+ segmentation results in 'betaT' space.
+
+BUG FIXES:
+
+ o plotTracks2(..., panels = "dh") gave an error due to a forgotten assignment.
+
+
+Version: 0.13.1 [2011-09-06]
+
+NEW FEATURES:
+
+ o Added formal class CBS, which holds the segmentation results returned by
+ segmentByCBS(). Several methods are available for CBS objects, e.g.
+ nbrOfLoci(), nbrOfSegments(), nbrOfChromosomes(), getChromosomes(),
+ estimateStandardDeviation() etc.
+
+ o Now segmentByCBS() always returns a CBS object. To coerce to a DNAcopy
+ object (as defined in the DNAcopy class) use as.DNAcopy().
+
+ o Added coerce methods as.DNAcopy() for CBS objects and as.CBS() for DNAcopy
+ objects.
+
+
+Version: 0.13.0 [2011-09-01]
+
+NEW FEATURES:
+
+ o GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.
+
+ o Added append() for CBS objects.
+
+BUG FIXES:
+
+ o Internal methods plotTracksManyChromosomes() and tileChromosomes() for CBS
+ did not work at all and therefore neither plotTracks() for CBS with more
+ than one chromosome.
+
+
+Version: 0.12.2 [2011-08-27]
+
+CODE REFACTORING:
+
+ o CLEANUP: Now R CMD check is no longer giving a note that the package loads
+ package 'DNAcopy' in .onAttach().
+
+
+Version: 0.12.1 [2011-08-08]
+
+BUG FIXES:
+
+ o If dropSegmentationOutliers() would drop an outlier next to a change point,
+ such that the total copy-number signal becomes NA, then the sanity checks
+ that TCN segments always overlaps DH segments would fail. Now the sanity
+ checks are aware of this special case. These sanity checks were moved from
+ bootstrapTCNandDHByRegion() to segmentByPairedPSCBS(). Thanks Christine To
+ at University of Toronto for reporting on this.
+
+
+Version: 0.12.0 [2011-07-23]
+
+BUG FIXES:
+
+ o Recently R devel automatically adds a namespace to a package, if missing.
+ This caused some of the PSCBS examples to throw an exception related to
+ incorrect dispatching of cat().
+
+CODE REFACTORING:
+
+ o Added a namespace to the package, which will be more or less a requirement
+ in the next major release of R.
+
+
+Version: 0.11.7 [2011-07-15]
+
+DOCUMENTATION:
+
+ o Added a section to help("segmentByPairedPSCBS") on the importance of doing
+ a whole-genome PSCBS segmentations if calling AB and LOH states afterward.
+
+ o Made it more clear in help("segmentByPairedPSCBS") that arguments 'betaT',
+ 'betaN' and 'muN' may contain NAs for non-polymorphic loci.
+
+
+Version: 0.11.6 [2011-07-14]
+
+BUG FIXES:
+
+ o ROBUSTNESS: In some cases, the segmentation table would contain column names
+ with incorrect capitalization, e.g. "tcnnbrOfLoci" instead of "tcnNbrOfLoci".
+ This would cause several downstream methods to give an error. The reason
+ for this is that the Hmisc package, if loaded after R.utils, overrides
+ capitalize() in R.utils with another (buggy?) capitalize() function.
+ To avoid this, we now everywhere specify explicitly that we want the one in
+ R.utils. Thanks Christine To at University of Toronto for reporting on this.
+
+
+Version: 0.11.5 [2011-07-10]
+
+BUG FIXES:
+
+ o tileChromosomes() for PairedPSCBS was still assuming the old naming
+ convention of column names. This caused plotTracks() to throw an exception
+ when plotting multiple chromosomes.
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Fixed partial argument matchings in arrowsC1C2() and
+ arrowsDeltaC1C2() for PairedPSCBS.
+
+
+Version: 0.11.4 [2011-07-07]
+
+NEW FEATURES:
+
+ o GENERALIZATION: Now the internal estimator function that estimateDeltaLOH()
+ uses returns -Inf if all segments are called AB, instead of throwing an
+ exception. This will in turn make callLOH() call all segments to be non-LOH.
+
+DOCUMENTATION:
+
+ o Removed obsolete references to the R-forge repository.
+
+BUG FIXES:
+
+ o Consecutive calls to callAB(..., force = TRUE) would append additional
+ 'abCall' columns to the segmentation table instead of replacing existing
+ calls.
+
+
+Version: 0.11.3 [2011-07-06]
+
+NEW FEATURES:
+
+ o ROBUSTNESS: Added a sanity check to estimateDeltaLOHByMinC1AtNonAB() for
+ PairedPSCBS object. The test asserts that there exist segments that are not
+ in allelic balance, which are needed in order to estimate DeltaLOH.
+
+DOCUMENTATION:
+
+ o The description of argument 'chromosome' for segmentByPairedPSCBS() did not
+ describe how to segment multiple chromosomes in one call.
+
+
+Version: 0.11.2 [2011-07-05]
+
+BUG FIXES:
+
+ o Output fields 'tcnNbrOfSNPs' and 'tcnNbrOfHets' were mistakenly labeled as
+ 'tcnNbrOr...'. Thanks Christine Ho at UC Berkeley for reporting on this.
+
+
+Version: 0.11.1 [2011-06-28]
+
+DOCUMENTATION:
+
+ o Clarified that argument 'CT' should be tumor copy number ratios relative to
+ the normal.
+
+ o Added Rd help for as.data.frame() of PairedPSCBS.
+
+
+Version: 0.11.0 [2011-06-14]
+
+SIGNIFICANT CHANGES:
+
+ o Renamed all column names of returned data frames such that they follow the
+ camelCase naming conventions in addition to be somewhat shorter too.
+
+NEW FEATURES:
+
+ o GENERALIZATION: Added argument 'columnNamesFlavor' to segmentByCBS().
+
+
+Version: 0.10.2 [2011-06-07]
+
+CODE REFACTORING:
+
+ o CLEANUP: Cleaned up the example():s.
+
+ o Added more biocViews categories to DESCRIPTION
+
+
+Version: 0.10.1 [2011-05-31]
+
+NEW FEATURES:
+
+ o GENERALIZATION: The package can now be *installed* without the DNAcopy
+ package being installed. If package is loaded without DNAcopy installed,
+ an informative message will explain how to install it.
+
+ o Added installDNAcopy(), which will install DNAcopy from Bioconductor.
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Now all DNAcopy functions are called as DNAcopy::nnn().
+
+
+Version: 0.10.0 [2011-05-29]
+
+SIGNIFICANT CHANGES:
+
+ o Renamed package to PSCBS (from 'psCBS').
+
+ o Renamed all arguments, variables, and functions referring to 'tau' to refer
+ to 'delta' reflecting the notation of the Paired PSCBS paper.
+
+ o Renamed options, example code and help pages to reflect new package name.
+
+DOCUMENTATION:
+
+ o Updated references in help pages.
+
+ o Now the paired PSCBS is formally referred to as 'Paired PSCBS'.
+
+
+Version: 0.9.54 [2011-04-27]
+
+NEW FEATURES:
+
+ o Added argument 'maxC' to estimateTauLOHByMinC1ForNonAB().
+
+
+Version: 0.9.53 [2011-04-14]
+
+ o Added argument 'max' to estimateTauAB() and estimateTauLOH().
+
+
+Version: 0.9.52 [2011-04-14]
+
+BUG FIXES:
+
+ o Argument 'minSize' of callAB() and callLOH() had no effect.
+
+
+Version: 0.9.51 [2011-04-12]
+
+NEW FEATURES:
+
+ o Added argument 'minSize' to callAB() and callLOH() for PairedPSCBS.
+
+ o Now the a conflicting call in callLOH()/callAB() with argument
+ xorCalls = TRUE is set to NA to contrast it from a FALSE call.
+
+
+Version: 0.9.50 [2011-04-12]
+
+NEW FEATURES:
+
+ o Added argument 'xorCalls' to callLOH() and callAB() for PairedPSCBS. When
+ TRUE (the default), a segment that is already called AB will never be called
+ LOH, and vice versa.
+
+
+Version: 0.9.49 [2011-04-11]
+
+NEW FEATURES:
+
+ o Updated estimateTauABBySmallDH() for PairedPSCBS to use a "symmetric"
+ quantile estimator.
+
+ o Added argument 'midpoint' to estimateTauLOHByMinC1AtNonAB().
+
+BUG FIXES:
+
+ o The recent callLOH() would not store the LOH calls.
+
+
+Version: 0.9.48 [2011-04-10]
+
+NEW FEATURES:
+
+ o Added callLOH() for PairedPSCBS, which in turn calls auxiliary methods.
+
+ o Added estimateTauLOH() for PairedPSCBS, which in turn calls axillary methods.
+
+ o Now callAB(..., force = FALSE) skips the caller if allelic-balance calls
+ already exist.
+
+DOCUMENTATION:
+
+ o Update the example for segmentByPairedPSCBS to reflect the restructured AB
+ and LOH callers.
+
+
+Version: 0.9.47 [2011-04-08]
+
+NEW FEATURES:
+
+ o Added estimateTauABBySmallDH()
+
+ o Added internal weightedQuantile().
+
+DOCUMENTATION:
+
+ o Added help pages for more methods.
+
+CODE REFACTORING:
+
+ o CLEANUP: Started to restructure the source code files.
+
+
+Version: 0.9.46 [2011-04-08]
+
+BUG FIXES:
+
+ o postsegmentTCN() for PairedPSCBS could generate an invalid 'tcnSegRows'
+ matrix, where the indices for two consecutive segments would overlap, which
+ is invalid. This was caught with real data, but it seems to have required a
+ very rare combination of data in order for it to occur.
+
+
+Version: 0.9.45 [2011-04-05]
+
+BUG FIXES:
+
+ o estimateHighDHQuantileAtAB() for PairedPSCBS would throw an error on an
+ undefined 'trim' if verbose output was used.
+
+
+Version: 0.9.44 [2011-02-18]
+
+NEW FEATURES:
+
+ o Added estimateHighDHQuantileAtAB() for PairedPSCBS.
+
+
+Version: 0.9.43 [2011-02-06]
+
+BUG FIXES:
+
+ o plotTracks2() queried non-existing argument 'tracks'.
+
+
+Version: 0.9.42 [2011-02-03]
+
+NEW FEATURES:
+
+ o Added estimateKappa() for estimating the normal contamination.
+
+
+Version: 0.9.41 [2011-02-02]
+
+SIGNFICANT CHANGES:
+
+ o Updated default for 'tauAB' of callABandHighAI() and callABandLowC1() to be
+ estimated from data using estimateTauAB().
+
+NEW FEATURES:
+
+ o Added argument 'tauTCN' to estimateTauAB().
+
+
+Version: 0.9.40 [2011-01-27]
+
+NEW FEATURES:
+
+ o Added argument 'flavor' to estimateTauAB() for estimating the AB threshold
+ using alternative methods.
+
+
+Version: 0.9.39 [2011-01-19]
+
+NEW FEATURES:
+
+ o Added trial version of new plotTracks2(), which will later replace
+ plotTracks(). Currently it only works for single chromosomes.
+
+ o Added support functions, e.g. updateMeans().
+
+
+Version: 0.9.38 [2011-01-18]
+
+NEW FEATURES:
+
+ o Added arguments 'changepoints' and 'col' to plotTracks() for PairedPSCBS.
+
+ o Now plotTracks(..., add = FALSE) for PairedPSCBS only sets up subplots if
+ argument 'tracks' specifies more than one panel.
+
+DOCUMENTATION:
+
+ o Documented more plotTracks() arguments for PairedPSCBS.
+
+BUG FIXES:
+
+ o Now plotTracks(..., add = TRUE) for PairedPSCBS plots to the current
+ figure/panel.
+
+
+Version: 0.9.37 [2011-01-18]
+
+BUG FIXES:
+
+ o 'tcnSegRows' and 'dhSegRows' where not updated by extractByRegions() for
+ PairedPSCBS.
+
+
+Version: 0.9.36 [2011-01-14]
+
+NEW FEATURES:
+
+ o Added estimateTauAB() for estimating the tauAB tuning parameter when calling
+ segments in allelic balance. Updated example(segmentByPairedPSCBS) to
+ illustrate how to use it.
+
+ o Added extractByRegions() for PairedPSCBS.
+
+
+Version: 0.9.35 [2011-01-12]
+
+NEW FEATURES:
+
+ o Now postsegmentTCN(..., force = TRUE) for PairedPSCBS also updates the TCN
+ estimates even for segments where the DH segmentation did not find any
+ additional change points.
+
+
+Version: 0.9.34 [2010-12-09]
+
+BUG FIXES:
+
+ o When there were multiple chromosomes processed by segmentByPairedPSCBS(),
+ then the returned data object would contain 'betaT' identical to 'betaTN'.
+
+
+Version: 0.9.33 [2010-12-07]
+
+NEW FEATURES:
+
+ o Added callLowC1ByC1() and callABandLowC1().
+
+
+Version: 0.9.32 [2010-12-03]
+
+BUG FIXES:
+
+ o In rare cases the bootstrap sanity checks can indeed produce an invalid
+ 'range', more precisely where (range[,2] >= range[,1]) is not true. This
+ can happen if there is no variation in the bootstrap estimates. Because of
+ this we allow for some tolerance.
+
+
+Version: 0.9.31 [2010-12-02]
+
+NEW FEATURES:
+
+ o Added option "psCBS/sanityChecks/tolerance" for specifying the tolerance of
+ some internal sanity checks.
+
+
+Version: 0.9.30 [2010-12-01]
+
+CODE REFACTORING:
+
+ o Rewrote all code dealing with the identification of loci belong to segments.
+ The code is now utilizing the 'segRows' element returned by
+ DNAcopy::segment(). Lots of the code was rewritten and therefore completely
+ new bugs may have been introduced.
+
+
+Version: 0.9.25 [2010-11-30]
+
+BUG FIXES:
+
+ o Argument 'flavor' of segmentByPairedPSCBS() would be ignored if multiple
+ chromosomes were segmented.
+
+ o extractByChromosome() for PSCBS would call it self instead of
+ extractByChromosomes().
+
+
+Version: 0.9.24 [2010-11-28]
+
+BUG FIXES:
+
+ o postsegmentTCN() did not handle loci with the same positions and that are
+ split in two different segments. It also did not exclude loci with missing
+ values.
+
+
+Version: 0.9.23 [2010-11-28]
+
+BUG FIXES:
+
+ o The algorithm in segmentByCBS() that infers which loci (of the ones share
+ the same genomic positions) that should be exclude from each segment did not
+ take missing signals into account.
+
+ o Iff argument 'chromosome' to segmentByPairedPSCBS() was of length greater
+ than one and specified exactly one unique chromosome, then exception
+ "Number of elements in argument 'chromosome' should be exactly 8712 not
+ 86209 value(s)" would be thrown.
+
+
+Version: 0.9.22 [2010-11-27]
+
+BUG FIXES:
+
+ o bootstrapTCNandDHByRegion() would incorrectly include non-polymorphic loci
+ in the set of homozygous SNPs during resampling.
+
+ o segmentByPairedPSCBS() would not accept missing values in argument
+ 'chromosome'.
Version: 0.9.21 [2010-11-27]
-o Now arguments '...' of segmentByPairedPSCBS() are passed to
- the two segmentByCBS() calls.
-o Added callSegmentationOutliers(), which can be used to identify
- single-locus outliers that have a genomic signal that is clearly
- outside the expected range. The dropSegmentationOutliers() sets
- locus outliers detected by this method to missing values.
- This is useful for excluding total copy-number outliers that
- otherwise can have a dramatic impact on the non-robust CBS method.
+
+NEW FEATURES:
+
+ o Now arguments '...' of segmentByPairedPSCBS() are passed to the two
+ segmentByCBS() calls.
+
+ o Added callSegmentationOutliers(), which can be used to identify single-locus
+ outliers that have a genomic signal that is clearly outside the expected
+ range. The dropSegmentationOutliers() sets locus outliers detected by this
+ method to missing values. This is useful for excluding total copy-number
+ outliers that otherwise can have a dramatic impact on the non-robust CBS
+ method.
Version: 0.9.20 [2010-11-26]
-o Added optional argument 'chromosomes' to plotTracks() to plot a
- subset of all chromosomes.
-o Added extractByChromosomes() for PSCBS.
-o Now the default confidence intervals for plotTracks() is (0.05,0.95),
- if existing.
-o Now all call functions estimate symmetric bootstrap quantiles for
- convenience of plotting confidence intervals.
-o BUG FIX: callABandHighAI() for PairedPSCBS used the old DH-only
- bootstrap method.
-o BUG FIX: The statistical sanity checks of the bootstrap estimates
- would give an error when only single-sided bootstrap confidence
- interval was calculated.
-o BUG FIX: The call functions, for instance callABandHighAI(), would throw
- 'Error in quantile.default(x, probs = alpha) : missing values and NaN's
- not allowed if 'na.rm' is FALSE' unless bootstrapTCNandDHByRegion() was
- run before.
+
+NEW FEATURES:
+
+ o Added optional argument 'chromosomes' to plotTracks() to plot a subset of
+ all chromosomes.
+
+ o Added extractByChromosomes() for PSCBS.
+
+ o Now the default confidence intervals for plotTracks() is (0.05,0.95), if
+ existing.
+
+ o Now all call functions estimate symmetric bootstrap quantiles for
+ convenience of plotting confidence intervals.
+
+BUG FIXES:
+
+ o callABandHighAI() for PairedPSCBS used the old DH-only bootstrap method.
+
+ o The statistical sanity checks of the bootstrap estimates would give an error
+ when only single-sided bootstrap confidence interval was calculated.
+
+ o The call functions, for instance callABandHighAI(), would throw 'Error in
+ quantile.default(x, probs = alpha) : missing values and NaN's not allowed if
+ 'na.rm' is FALSE' unless bootstrapTCNandDHByRegion() was run before.
Version: 0.9.19 [2010-11-23]
-o ROBUSTNESS: Added more sanity checks to bootstrapTCNandDHByRegion().
-o WORKAROUND: The precision of the mean levels of DNAcopy::segment()
- is not great enough to always compare it to that of R's estimates.
-o BUG FIX: bootstrapTCNandDHByRegion() would give an error if there was
- only one segment.
-o BUG FIX: segmentByPairedPSCBS() and bootstrapTCNandDHByRegion()
- would not subset the correct set of DH signals if there were some
- missing values in TCN.
+
+NEW FEATURES:
+
+ o ROBUSTNESS: Added more sanity checks to bootstrapTCNandDHByRegion().
+
+ o WORKAROUND: The precision of the mean levels of DNAcopy::segment() is not
+ great enough to always compare it to that of R's estimates.
+
+BUG FIXES:
+
+ o bootstrapTCNandDHByRegion() would give an error if there was only one
+ segment.
+
+ o segmentByPairedPSCBS() and bootstrapTCNandDHByRegion() would not subset the
+ correct set of DH signals if there were some missing values in TCN.
Version: 0.9.18 [2010-11-22]
-o Added argument 'calls' to plotTracks() for highlighting called regions.
-o Updated callAllelicBalanceByDH() and callExtremeAllelicImbalanceByDH()
- to utilize bootstrapTCNandDHByRegion().
-o ROBUSTNESS: Now drawConfidenceBands() of PairedPSCBS silently does
- nothing if the requested bootstrap quantiles are available.
-o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would not
- correctly detect if bootstrap results are already available.
+
+NEW FEATURES:
+
+ o Added argument 'calls' to plotTracks() for highlighting called regions.
+
+ o Updated callAllelicBalanceByDH() and callExtremeAllelicImbalanceByDH() to
+ utilize bootstrapTCNandDHByRegion().
+
+ o ROBUSTNESS: Now drawConfidenceBands() of PairedPSCBS silently does nothing
+ if the requested bootstrap quantiles are available.
+
+BUG FIXES:
+
+ o bootstrapTCNandDHByRegion() for PairedPSCBS would not correctly detect if
+ bootstrap results are already available.
Version: 0.9.17 [2010-11-21]
-o Now plotTracks() supports tracks "tcn,c1", "tcn,c2" and "c1,c2" too.
-o Added support for flavor "tcn&dh" in segmentByPairedPSCBS(), which
- contrary to "tcn,dh" enforces TCN and DH to have the same change
- points. The default flavor is now "tcn&dh".
-o Added argument 'xlim' to plotTracks() making it possible to zoom in.
+
+NEW FEATURES:
+
+ o Now plotTracks() supports tracks "tcn,c1", "tcn,c2" and "c1,c2" too.
+
+ o Added support for flavor "tcn&dh" in segmentByPairedPSCBS(), which contrary
+ to "tcn,dh" enforces TCN and DH to have the same change points. The default
+ flavor is now "tcn&dh".
+
+ o Added argument 'xlim' to plotTracks() making it possible to zoom in.
Version: 0.9.16 [2010-11-21]
-o Now joinSegments=TRUE is the default for segmentByCBS() and
- segmentByPairedPSCBS().
-o Added argument 'quantiles' to plotTracks(), which if specified
- draws confidence bands previously estimated from bootstrapping.
-o Added drawConfidenceBands() for PairedPSCBS.
-o Added bootstrapTCNandDHByRegion() for PairedPSCBS.
-o Added standalone joinSegments() for CBS results.
-o Now segmentByPairedPSCBS() also returns minor and major
- copy numbers for each segment.
+
+NEW FEATURES:
+
+ o Now joinSegments = TRUE is the default for segmentByCBS() and
+ segmentByPairedPSCBS().
+
+ o Added argument 'quantiles' to plotTracks(), which if specified draws
+ confidence bands previously estimated from bootstrapping.
+
+ o Added drawConfidenceBands() for PairedPSCBS.
+
+ o Added bootstrapTCNandDHByRegion() for PairedPSCBS.
+
+ o Added standalone joinSegments() for CBS results.
+
+ o Now segmentByPairedPSCBS() also returns minor and major copy numbers for
+ each segment.
Version: 0.9.15 [2010-11-21]
-o Adjusted postsegmentTCN() such that the updated TCN segment boundaries
- are the maximum of the DH segment and the support by the loci. This
- means that postsegmentTCN() will work as expected both when signals
- where segmented with 'joinSegments' being TRUE or FALSE.
-o Updated plotTracks() for PairedPSCBS such that the TCN segmentation
- is colored 'purple' and the DH segmentation 'orange' for TCN and DH
- only tracks.
+
+NEW FEATURES:
+
+ o Adjusted postsegmentTCN() such that the updated TCN segment boundaries are
+ the maximum of the DH segment and the support by the loci. This means that
+ postsegmentTCN() will work as expected both when signals where segmented
+ with 'joinSegments' being TRUE or FALSE.
+
+ o Updated plotTracks() for PairedPSCBS such that the TCN segmentation is
+ colored 'purple' and the DH segmentation 'orange' for TCN and DH only tracks.
Version: 0.9.14 [2010-11-20]
-o Now it is possible to specify the boundaries of the regions to
- be segmented as known change points via argument 'knownCPs'.
-o Added argument 'joinSegments' to segmentByCBS() and
- segmentByPairedPSCBS() in order to specify if neighboring
- segments should be joined or not.
-o Now segmentByCBS() and segmentByPairedPSCBS() allow for
- unknown genomic positions as well as missing total CN signals.
+
+NEW FEATURES:
+
+ o Now it is possible to specify the boundaries of the regions to be segmented
+ as known change points via argument 'knownCPs'.
+
+ o Added argument 'joinSegments' to segmentByCBS() and segmentByPairedPSCBS()
+ in order to specify if neighboring segments should be joined or not.
+
+ o Now segmentByCBS() and segmentByPairedPSCBS() allow for unknown genomic
+ positions as well as missing total CN signals.
Version: 0.9.13 [2010-11-19]
-o Added argument 'joinSegments' to segmentByCBS() in order to specify
- if neighboring segments should be joined or not.
+
+NEW FEATURES:
+
+ o Added argument 'joinSegments' to segmentByCBS() in order to specify if
+ neighboring segments should be joined or not.
Version: 0.9.12 [2010-11-19]
-o Added plotTracks() and drawLevels() etc to CBS results.
-o Now segmentByCBS() allows for unknown genomic positions.
-o Now segmentByCBS() allows for missing signals.
-o Added argument 'preserveOrder' to segmentByCBS(). If TRUE, then
- the loci in the returned 'data' object are ordered as the input
- data, otherwise it is ordered along the genome.
+
+NEW FEATURES:
+
+ o Added plotTracks() and drawLevels() etc to CBS results.
+
+ o Now segmentByCBS() allows for unknown genomic positions.
+
+ o Now segmentByCBS() allows for missing signals.
+
+ o Added argument 'preserveOrder' to segmentByCBS(). If TRUE, then the loci in
+ the returned 'data' object are ordered as the input data, otherwise it is
+ ordered along the genome.
Version: 0.9.11 [2010-11-16]
-o Now the 'data' object returned by segmentByCBS() contains field
- 'index' if and only if the loci had to be reorder along the genome.
-o DOCUMENTATION: Added more details, references to papers, and cross
- links to other functions to the help pages.
-o BUG FIX: In the rare cases where two loci at the same positions are
- split up into two neighboring segments, then segmentByPairedPSCBS()
- would fail to infer which they were if and only if the loci were not
- ordered along the genome. This could happen with for instance
- Affymetrix GenomeWideSNP_6 data.
+
+NEW FEATURES:
+
+ o Now the 'data' object returned by segmentByCBS() contains field 'index' if
+ and only if the loci had to be reorder along the genome.
+
+DOCUMENTATION:
+
+ o Added more details, references to papers, and cross links to other functions
+ to the help pages.
+
+BUG FIXES:
+
+ o In the rare cases where two loci at the same positions are split up into two
+ neighboring segments, then segmentByPairedPSCBS() would fail to infer which
+ they were if and only if the loci were not ordered along the genome. This
+ could happen with for instance Affymetrix GenomeWideSNP_6 data.
Version: 0.9.10 [2010-11-09]
-o Added argument 'cex=1' to plotTracks().
-o BUG FIX: It was not possible to plot BAF tracks with plotTracks().
+
+NEW FEATURES:
+
+ o Added argument 'cex = 1' to plotTracks().
+
+BUG FIXES:
+
+ o It was not possible to plot BAF tracks with plotTracks().
Version: 0.9.9 [2010-11-05]
-o BUG FIX: segmentByCBS() tried to pass non-existing argument
- 'undo.split' to DNAcopy::segment(). It should be 'undo.splits'.
+
+BUG FIXES:
+
+ o segmentByCBS() tried to pass non-existing argument 'undo.split' to
+ DNAcopy::segment(). It should be 'undo.splits'.
Version: 0.9.8 [2010-11-04]
-o BUG FIX: There was a stray/debug stop() statement left in
- segmentByPairedPSCBS() causing an "error" in the rare case
- when loci that have the same physical locations are split
- into two different segments.
+
+BUG FIXES:
+
+ o There was a stray/debug stop() statement left in segmentByPairedPSCBS()
+ causing an "error" in the rare case when loci that have the same physical
+ locations are split into two different segments.
Version: 0.9.7 [2010-11-03]
-o ROBUSTNESS: Now bootstrapDHByRegion() uses resample() of R.utils.
-o BUG FIX: bootstrapDHByRegion() did not sample from the correct
- unit(s) when there was only one DH signal.
+
+ o ROBUSTNESS: Now bootstrapDHByRegion() uses resample() of R.utils.
+
+BUG FIXES:
+
+ o bootstrapDHByRegion() did not sample from the correct unit(s) when there was
+ only one DH signal.
Version: 0.9.6 [2010-11-02]
-o Added arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS().
-o Added argument 'undo' to segmentByCBS(), which corresponds to
- undo.splits="sdundo" and undo.SD=undo, if undo < +Inf.
-o BUG FIX: Arguments 'alphaTCN' and 'alphaDH' of segmentByPairedPSCBS()
- were not used when more than one chromosome were segmented.
+
+NEW FEATURES:
+
+ o Added arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS().
+
+ o Added argument 'undo' to segmentByCBS(), which corresponds to
+ undo.splits = "sdundo" and undo.SD = undo, if undo < +Inf.
+
+BUG FIXES:
+
+ o Arguments 'alphaTCN' and 'alphaDH' of segmentByPairedPSCBS() were not used
+ when more than one chromosome were segmented.
Version: 0.9.5 [2010-11-01]
-o Added arguments 'alphaAB' and 'alphaHighAI' to callABandHighAI().
-o BUG FIX: bootstrapDHByRegion() would give an error if only a single
- quantile was requested.
-o BUG FIX: bootstrapDHByRegion() would give "Error in if (nbrOfUnits
- > segJJ[, "dh.num.mark"]) { : missing value where TRUE/FALSE needed"
- when 'dh.num.mark' was NA.
+
+NEW FEATURES:
+
+ o Added arguments 'alphaAB' and 'alphaHighAI' to callABandHighAI().
+
+BUG FIXES:
+
+ o bootstrapDHByRegion() would give an error if only a single quantile was
+ requested.
+
+ o bootstrapDHByRegion() would give "Error in if (nbrOfUnits > segJJ[,
+ "dh.num.mark"]) { : missing value where TRUE/FALSE needed" when
+ 'dh.num.mark' was NA.
Version: 0.9.4 [2010-10-25]
-o Now the default is a 95% confidence interval for calls.
-o Now segmentByCBS() also returns element 'lociNotPartOfSegment',
- if there are segments that share end points, which can happen if
- a change point is called in middle of a set of loci that have the
- same genomic positions. In such cases, 'lociNotPartOfSegment'
- specifies which loci are *not* part of which segment. Then by
- identifying the loci that are within a segment by their positions
- and excluding any of the above, one knows exactly which loci
- CBS included in each segment.
-o BUG FIX: Now bootstrapDHByRegion() for PairedPSCBS handles the
- rare case when markers with the same positions are split in
- two different segments.
-o BUG FIX: Now the correct set of loci are extracted from each TCN
- segment, in the rare case that two neighboring TCN segments have
- the same end points.
+
+NEW FEATURES:
+
+ o Now the default is a 95% confidence interval for calls.
+
+ o Now segmentByCBS() also returns element 'lociNotPartOfSegment', if there are
+ segments that share end points, which can happen if a change point is called
+ in middle of a set of loci that have the same genomic positions. In such
+ cases, 'lociNotPartOfSegment' specifies which loci are *not* part of which
+ segment. Then by identifying the loci that are within a segment by their
+ positions and excluding any of the above, one knows exactly which loci CBS
+ included in each segment.
+
+BUG FIXES:
+
+ o Now bootstrapDHByRegion() for PairedPSCBS handles the rare case when markers
+ with the same positions are split in two different segments.
+
+ o Now the correct set of loci are extracted from each TCN segment, in the rare
+ case that two neighboring TCN segments have the same end points.
Version: 0.9.3 [2010-10-25]
-o Added argument 'ciRange' to callAllelicBalance() and
- callExtremeAllelicImbalance().
-o BUG FIX: bootstrapDHByRegion() for PairedPSCBS would bootstrap
- from the incorrect set of loci when the DH region contained
- only one locus.
-o BUG FIX: bootstrapDHByRegion() for PairedPSCBS would bootstrap
- from the incorrect set of loci if more than one chromosome
- was available.
+
+NEW FEATURES:
+
+ o Added argument 'ciRange' to callAllelicBalance() and
+ callExtremeAllelicImbalance().
+
+BUG FIXES:
+
+ o bootstrapDHByRegion() for PairedPSCBS would bootstrap from the incorrect set
+ of loci when the DH region contained only one locus.
+
+ o bootstrapDHByRegion() for PairedPSCBS would bootstrap from the incorrect set
+ of loci if more than one chromosome was available.
Version: 0.9.2 [2010-10-24]
-o BUG FIX: plotTracks() would give "Error: object 'nbrOfLoci' not found'
- for whole-genome plots.
+
+BUG FIXES:
+
+ o plotTracks() would give "Error: object 'nbrOfLoci' not found' for
+ whole-genome plots.
Version: 0.9.1 [2010-10-20]
-o Now plotTracks() can plot whole-genome data.
+
+NEW FEATURES:
+
+ o Now plotTracks() can plot whole-genome data.
Version: 0.9.0 [2010-10-18]
-o Added arguments 'alphaTCN' and 'alphaDH' to segmentByPairedPSCBS()
- with defaults according to the paper.
+
+NEW FEATURES:
+
+ o Added arguments 'alphaTCN' and 'alphaDH' to segmentByPairedPSCBS() with
+ defaults according to the paper.
Version: 0.8.3 [2010-10-18]
-o Now segmentByPairedPSCBS() can segment multiple chromosomes.
+
+NEW FEATURES:
+
+ o Now segmentByPairedPSCBS() can segment multiple chromosomes.
Version: 0.8.2 [2010-10-17]
-o Added argument 'tbn' to segmentByPairedPSCBS() specifying whether
- TumorBoostNormalization should be applied or not.
+
+NEW FEATURES:
+
+ o Added argument 'tbn' to segmentByPairedPSCBS() specifying whether
+ TumorBoostNormalization should be applied or not.
Version: 0.8.1 [2010-10-10]
-o The default for segmentByPairedPSCBS() is now to segment TCN on
- the original scale, not the sqrt().
-o Added plotTracks() for PairedPSCBS.
+
+SIGNIFICANT CHANGES:
+
+ o The default for segmentByPairedPSCBS() is now to segment TCN on the original
+ scale, not the sqrt().
+
+NEW FEATURES:
+
+ o Added plotTracks() for PairedPSCBS.
Version: 0.8.0 [2010-10-06]
-o CLEAN UP: Removed all old code, native code and help pages.
+
+CODE REFACTORING:
+
+ o CLEAN UP: Removed all old code, native code and help pages.
Version: 0.7.8 [2010-10-03]
-o Added optional argument 'chromosome' to segmentByCBS().
- Note that at this point it is only used for annotating the
- results; it can not be used to segmented multiple chromosomes
- at ones.
+
+NEW FEATURES:
+
+ o Added optional argument 'chromosome' to segmentByCBS(). Note that at this
+ point it is only used for annotating the results; it can not be used to
+ segmented multiple chromosomes at ones.
Version: 0.7.7 [2010-09-26]
-o Now subsetBySegments() and postsegmentTCN() for PairedPSCBS
- handles multiple chromosomes.
+
+NEW FEATURES:
+
+ o Now subsetBySegments() and postsegmentTCN() for PairedPSCBS handles multiple
+ chromosomes.
Version: 0.7.6 [2010-09-24]
-o Added support to annotating and subsetting also by chromosomes,
- as well as appending segmentation results from different chromosomes
- together.
+
+NEW FEATURES:
+
+ o Added support to annotating and subsetting also by chromosomes, as well as
+ appending segmentation results from different chromosomes together.
Version: 0.7.5 [2010-09-21]
-o Added postsegmentTCN() for PairedPSCBS, which updates the
- TCN segment start and ends, estimates and counts given the
- DH segments.
+
+NEW FEATURES:
+
+ o Added postsegmentTCN() for PairedPSCBS, which updates the TCN segment start
+ and ends, estimates and counts given the DH segments.
Version: 0.7.4 [2010-09-18]
-o Added argument 'chromosome' to segmentByPairedPSCBS(), which, if given,
- adds a chromosome column to the data and segmentation results.
-o BUG FIX: plot() for PairedPSCBS used a non-defined variable.
+
+NEW FEATURES:
+
+ o Added argument 'chromosome' to segmentByPairedPSCBS(), which, if given, adds
+ a chromosome column to the data and segmentation results.
+
+BUG FIXES:
+
+ o plot() for PairedPSCBS used a non-defined variable.
Version: 0.7.3 [2010-09-16]
-o Added callABandHighAI() for calling paired PSCBS segmentation results.
-o Added internal bootstrapping functions.
+
+NEW FEATURES:
+
+ o Added callABandHighAI() for calling paired PSCBS segmentation results.
+
+CODE REFACTORING:
+
+ o Added internal bootstrapping functions.
Version: 0.7.2 [2010-09-15]
-o Added more methods for the PSCBS class.
+
+NEW FEATURES:
+
+ o Added more methods for the PSCBS class.
Version: 0.7.1 [2010-09-08]
-o Added more methods for the PSCBS class.
-o Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.
+
+NEW FEATURES:
+
+ o Added more methods for the PSCBS class.
+
+ o Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.
Version: 0.7.0 [2010-09-04]
-o Updated segmentByPairedPSCBS() to provide two-step segmentation
- from first segmenting the total copy numbers and then the
- decrease-of-heterozygosity signals. Added utility functions for
- plotting the results. The code for calling allelic imbalance
- and LOH is still to be added.
+
+NEW FEATURES:
+
+ o Updated segmentByPairedPSCBS() to provide two-step segmentation from first
+ segmenting the total copy numbers and then the decrease-of-heterozygosity
+ signals. Added utility functions for plotting the results. The code for
+ calling allelic imbalance and LOH is still to be added.
Version: 0.6.3 [2010-09-02]
-o ROBUSTNESS: Now segmentByCBS() also works if there are no data points.
+
+NEW FEATURES:
+
+ o Now segmentByCBS() also works if there are no data points.
Version: 0.6.2 [2010-07-14]
-o CLEAN UP: Added callNaiveHeterzygotes() which is a cleaned up
- version of findheterozygous(). Added an Rd example that asserts
- that the two are identical and compares the calls to those of
- aroma.light::callNaiveGenotypes().
+
+NEW FEATURES:
+
+ o Added callNaiveHeterzygotes() which is a cleaned up version of
+ findheterozygous(). Added Rd example that asserts that the two are identical
+ and compares the calls to those of aroma.light::callNaiveGenotypes().
Version: 0.6.1 [2010-07-09]
-o Added low-level segmentByPairedPSCBS(), which runs paired PSCBS
- segmentation on a single sample and a single chromosome.
- It only segments; it does not call segments. This is only
- a stub in the sense that it still does not adjust p-values etc.
-o Added low-level segmentByCBS(), which runs CBS segmentation
- on a single sample and a single chromosome.
-o BACKWARD COMPATIBILITY: Now psCNA() returns a list of length 8.
-o Reverted psSegment() back to v0.5.6.
+
+NEW FEATURES:
+
+ o Added low-level segmentByPairedPSCBS(), which runs paired PSCBS segmentation
+ on a single sample and a single chromosome. It only segments; it does not
+ call segments. This is only a stub in the sense that it still does not
+ adjust p-values etc.
+
+ o Added low-level segmentByCBS(), which runs CBS segmentation on a single
+ sample and a single chromosome.
+
+ o BACKWARD COMPATIBILITY: Now psCNA() returns a list of length 8.
+
+ o Reverted psSegment() back to v0.5.6.
Version: 0.6.0 [2010-07-08]
-o Now psSegmentPaired() returns a data frame (no longer a matrix).
-o CLEANUP: Major cleanup, i.e. renaming variables, reordering etc.
-o CLEANUP: Created psSegmentPaired() from psSegment().
-o ROBUSTNESS: Replaced all 1:n with seq(length=n) to deal with n == 0.
-o ROBUSTNESS: Now all list elements are referenced by name.
-o ROBUSTNESS: Now all iterator variables are written as ii, jj etc.
-o Using setMethodS3() of R.methodsS3 to define S3 method.
-o Dropping NAMESPACE while package is finished. This makes it
- easier to patch methods etc.
+
+NEW FEATURES:
+
+ o Now psSegmentPaired() returns a data frame (no longer a matrix).
+
+ o CLEANUP: Created psSegmentPaired() from psSegment().
+
+CODE REFACTORING:
+
+ o CLEANUP: Major cleanup, i.e. renaming variables, reordering etc.
+
+ o ROBUSTNESS: Replaced all 1:n with seq(length = n) to deal with n == 0.
+
+ o ROBUSTNESS: Now all list elements are referenced by name.
+
+ o ROBUSTNESS: Now all iterator variables are written as ii, jj etc.
+
+ o Using setMethodS3() of R.methodsS3 to define S3 method.
+
+ o Dropping NAMESPACE while package is finished. This makes it easier to patch
+ methods etc.
Version: 0.5.6 [2010-07-07]
-o Added example(psSegment).
-o BUG FIX: Previous clean up introduced bugs.
-o BUG FIX: The dynamic library for hrmode() was not loaded.
+
+DOCUMENTATION:
+
+ o Added example(psSegment).
+
+BUG FIXES:
+
+ o Previous clean up introduced bugs.
+
+ o The dynamic library for hrmode() was not loaded.
Version: 0.5.5 [2010-05-05]
-o CLEAN UP/ROBUSTNESS: Major code clean up.
+
+CODE REFACTORING:
+
+ o CLEAN UP/ROBUSTNESS: Major code clean up.
Version: 0.5.4 [2010-04-30]
-o Added internal hrmode().
-o CLEAN UP: Renamed source files to match function names.
- Only only function per source file.
+
+CODE REFACTORING:
+
+ o Added internal hrmode().
+
+ o CLEANUP: Renamed source files to match function names. Only only function
+ per source file.
Version: 0.5.3 [2010-04-22]
-o ABO updated the psCBS algorithm.
+
+SIGNIFICANT CHANGES:
+
+ o ABO updated the psCBS algorithm.
Version: 0.5.2 [2010-0?-??]
-o ???
+
+ o ???
Version: 0.5.1 [2010-03-31]
-o Now psSegment(..., matching.reference=TRUE) does TumorBoost
- normalization on the allele B fractions before segmentation.
+
+SIGNIFICANT CHANGES:
+
+ o Now psSegment(..., matching.reference = TRUE) does TumorBoost normalization
+ on the allele B fractions before segmentation.
Version: 0.5.0 [2010-03-12]
-o Added to R-forge repository.
+
+ o Added to R-forge repository.
diff --git a/R/CBS.CALL.R b/R/CBS.CALL.R
index a89d88e..6a82333 100644
--- a/R/CBS.CALL.R
+++ b/R/CBS.CALL.R
@@ -1213,9 +1213,6 @@ setMethodS3("mergeNonCalledSegments", "CBS", function(fit, ..., verbose=FALSE) {
setMethodS3("estimateDeltaCN", "CBS", function(fit, flavor=c("density(TCN)", "density(dTCN)", "dTCN"), adjust=0.3, ..., verbose=FALSE) {
- # This will load the 'aroma.light' namespace, if not already done.
- findPeaksAndValleys <- .use("findPeaksAndValleys", package="aroma.light");
-
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/R/CBS.R b/R/CBS.R
index 3eee1e8..f119341 100644
--- a/R/CBS.R
+++ b/R/CBS.R
@@ -620,7 +620,7 @@ setMethodS3("resegment", "CBS", function(fit, ..., verbose=FALSE) {
# (d) Merge
args <- formals;
args2 <- c(params, userArgs);
- for (kk in seq(along=args2)) {
+ for (kk in seq_along(args2)) {
value <- args2[[kk]];
if (!is.null(value)) {
key <- names(args2)[kk];
diff --git a/R/NonPairedPSCBS.R b/R/NonPairedPSCBS.R
index 073345c..603e457 100644
--- a/R/NonPairedPSCBS.R
+++ b/R/NonPairedPSCBS.R
@@ -343,7 +343,7 @@ setMethodS3("resegment", "NonPairedPSCBS", function(fit, ..., verbose=FALSE) {
# (d) Merge
args <- formals;
args2 <- c(params, userArgs);
- for (kk in seq(along=args2)) {
+ for (kk in seq_along(args2)) {
value <- args2[[kk]];
if (!is.null(value)) {
key <- names(args2)[kk];
diff --git a/R/PSCBS.isLocallyPhased.R b/R/PSCBS.isLocallyPhased.R
new file mode 100644
index 0000000..bea280b
--- /dev/null
+++ b/R/PSCBS.isLocallyPhased.R
@@ -0,0 +1,12 @@
+setMethodS3("isLocallyPhased", "PSCBS", function(fit, ...) {
+ segs <- getSegments(fit);
+ is.element("c1c2Swap", names(segs));
+})
+
+
+##############################################################################
+# HISTORY
+# 2014-03-24 [HB]
+# o Added isLocallyPhased() for PSCBS.
+# o Created.
+##############################################################################
diff --git a/R/PairedPSCBS.R b/R/PairedPSCBS.R
index cb8f093..ee4127b 100644
--- a/R/PairedPSCBS.R
+++ b/R/PairedPSCBS.R
@@ -53,7 +53,6 @@ setMethodS3("getLocusData", "PairedPSCBS", function(fit, ..., fields=c("asis", "
data$muN <- rep(NA_real_, times=length(data$rho))
data$muN[is.finite(data$rho)] <- 1/2
} else if (is.element("betaN", names)) {
- callNaiveGenotypes <- .use("callNaiveGenotypes", package="aroma.light");
data$muN <- callNaiveGenotypes(data$betaN);
} else {
throw("Cannot identify heterozygous SNPs or genotypes")
@@ -76,7 +75,6 @@ setMethodS3("getLocusData", "PairedPSCBS", function(fit, ..., fields=c("asis", "
# TumorBoost BAFs
if (!is.element("rhoN", names)) {
if (!is.element("betaTN", names) && is.element("betaN", names)) {
- normalizeTumorBoost <- .use("normalizeTumorBoost", package="aroma.light");
data$betaTN <- normalizeTumorBoost(betaN=data$betaN, betaT=data$betaT, muN=data$muN);
}
@@ -157,7 +155,7 @@ setMethodS3("resegment", "PairedPSCBS", function(fit, ..., verbose=FALSE) {
# (d) Merge
args <- formals;
args2 <- c(params, userArgs);
- for (kk in seq(along=args2)) {
+ for (kk in seq_along(args2)) {
value <- args2[[kk]];
if (!is.null(value)) {
key <- names(args2)[kk];
diff --git a/R/PairedPSCBS.callCopyNeutral.R b/R/PairedPSCBS.callCopyNeutral.R
index 6bcabd9..8f54bd5 100644
--- a/R/PairedPSCBS.callCopyNeutral.R
+++ b/R/PairedPSCBS.callCopyNeutral.R
@@ -196,6 +196,9 @@ setMethodS3("calcStatsForCopyNeutralABs", "PairedPSCBS", function(fit, ..., forc
# \arguments{
# \item{scale}{A @numeric scale factor in (0,Inf) used for rescaling
# (multiplying) the final estimate with.}
+# \item{flavor}{Specifies which type of estimator should be used.}
+# \item{kappa}{Estimate of background signal (used by the \code{"1-kappa"} method).}
+# \item{adjust, quantile}{Tuning parameters (used by the \code{"delta(mode)"} method).}
# \item{...}{Not used.}
# }
#
@@ -219,17 +222,71 @@ setMethodS3("calcStatsForCopyNeutralABs", "PairedPSCBS", function(fit, ..., forc
#
# @keyword internal
#*/###########################################################################
-setMethodS3("estimateDeltaCN", "PairedPSCBS", function(fit, scale=1, kappa=estimateKappa(fit), ...) {
+setMethodS3("estimateDeltaCN", "PairedPSCBS", function(fit, scale=1, flavor=c("1-kappa", "delta(mode)"), kappa=estimateKappa(fit), adjust=0.2, quantile=0.95, ...) {
# Argument 'scale':
disallow <- c("NA", "NaN", "Inf");
scale <- Arguments$getDouble(scale, range=c(0,Inf), disallow=disallow);
- # Argument 'kappa':
- disallow <- c("NA", "NaN", "Inf");
- kappa <- Arguments$getDouble(kappa, range=c(0,1), disallow=disallow);
+ # Argument 'flavor':
+ flavor <- match.arg(flavor);
+
- # Half a TCN unit length
- delta <- (1-kappa)/2;
+ if (flavor == "1-kappa") {
+ # Argument 'kappa':
+ disallow <- c("NA", "NaN", "Inf");
+ kappa <- Arguments$getDouble(kappa, range=c(0,1), disallow=disallow);
+
+ # Half a TCN unit length
+ delta <- (1-kappa)/2;
+ } else if (flavor == "delta(mode)") {
+ # To please R CMD check
+ rohCall <- abCall <- type <- NULL;
+ rm(list=c("rohCall", "abCall", "type"));
+
+ segs <- getSegments(fit);
+ segs <- subset(segs, !rohCall);
+ segs <- subset(segs, !abCall);
+ sigmas <- list();
+ for (name in c("c1", "c2", "tcn")) {
+ # FIXME/AD HOC: Here we assume certain fields
+ fields <- sprintf("%s_%s%%", name, c(5,95));
+ if (all(is.element(fields, names(segs)))) {
+ sigma <- segs[,fields[2]] - segs[,fields[1]];
+ } else {
+ if (name == "tcn") {
+ n <- segs[,"tcnNbrOfLoci"];
+ } else {
+ n <- segs[,"dhNbrOfLoci"];
+ n <- segs[,"tcnNbrOfLoci"];
+ }
+ n <- segs[,"tcnEnd"] - segs[,"tcnStart"];
+ sigma <- 1/sqrt(n);
+ }
+ sigmas[[name]] <- sigma;
+ }
+ segs <- segs[,c("c1Mean", "c2Mean", "tcnMean")];
+ x <- unlist(segs, use.names=FALSE);
+ w <- 1/unlist(sigmas, use.names=FALSE);
+ keep <- is.finite(x) & is.finite(w);
+ x <- x[keep]; w <- w[keep];
+ w <- w / sum(w);
+ d <- density(x, weights=w, adjust=adjust);
+## plotDensity(d);
+ tolMax <- max(d$y, na.rm=TRUE);
+ tols <- seq(from=tolMax, to=0, length.out=100);
+ stats <- data.frame(tolerance=tols, delta=NA_real_, count=NA_integer_);
+ for (kk in seq_along(tols)) {
+ tol <- tols[kk];
+ px <- subset(findPeaksAndValleys(d, tol=tol), type == "peak")$x;
+ nx <- length(px);
+ dx <- mean(diff(px));
+ stats[kk,"delta"] <- dx;
+ stats[kk,"count"] <- nx;
+ }
+ stats <- subset(stats, is.finite(delta));
+## print(stats);
+ delta <- median(stats[,"delta"]);
+ }
# Rescale
delta <- scale * delta;
diff --git a/R/PairedPSCBS.estimateKappa.R b/R/PairedPSCBS.estimateKappa.R
index 2e1ebb3..26b6cac 100644
--- a/R/PairedPSCBS.estimateKappa.R
+++ b/R/PairedPSCBS.estimateKappa.R
@@ -126,9 +126,6 @@ setMethodS3("estimateKappa", "PairedPSCBS", function(this, flavor=c("density(C1)
# @keyword internal
#*/###########################################################################
setMethodS3("estimateKappaByC1Density", "PairedPSCBS", function(this, typeOfWeights=c("dhNbrOfLoci", "sqrt(dhNbrOfLoci)"), adjust=1, from=0, minDensity=0.2, ..., verbose=FALSE) {
- findPeaksAndValleys <- .use("findPeaksAndValleys", package="aroma.light");
-
-
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/R/callSegmentationOutliers.R b/R/callSegmentationOutliers.R
index 5e2d746..9810093 100644
--- a/R/callSegmentationOutliers.R
+++ b/R/callSegmentationOutliers.R
@@ -57,10 +57,6 @@
# @keyword IO
#*/###########################################################################
setMethodS3("callSegmentationOutliers", "default", function(y, chromosome=0, x=NULL, method="DNAcopy::smooth.CNA", ..., verbose=FALSE) {
- # Local copies of DNAcopy functions
- CNA <- .use("CNA", package="DNAcopy");
- smooth.CNA <- .use("smooth.CNA", package="DNAcopy");
-
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/R/findNeutralCopyNumberState.R b/R/findNeutralCopyNumberState.R
index 21f55a6..64cec01 100644
--- a/R/findNeutralCopyNumberState.R
+++ b/R/findNeutralCopyNumberState.R
@@ -31,10 +31,6 @@
# @keyword internal
#*/###########################################################################
setMethodS3("findNeutralCopyNumberState", "default", function(C, isAI, weights=NULL, ..., minDensity=1e-10, flavor=c("firstPeak", "maxPeak"), verbose=FALSE) {
- # This will load the 'aroma.light' namespace, if not already done.
- findPeaksAndValleys <- .use("findPeaksAndValleys", package="aroma.light");
-
-
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/R/segmentByCBS.R b/R/segmentByCBS.R
index b9f072a..5801f2e 100644
--- a/R/segmentByCBS.R
+++ b/R/segmentByCBS.R
@@ -115,11 +115,6 @@
# @keyword IO
#*/###########################################################################
setMethodS3("segmentByCBS", "default", function(y, chromosome=0L, x=NULL, index=seq_along(y), w=NULL, undo=0, avg=c("mean", "median"), ..., joinSegments=TRUE, knownSegments=NULL, seed=NULL, verbose=FALSE) {
- # Local copies of DNAcopy functions
- getbdry <- .use("getbdry", package="DNAcopy");
- CNA <- .use("CNA", package="DNAcopy");
- segment <- .use("segment", package="DNAcopy");
-
R_SANITY_CHECK <- TRUE;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/R/segmentByNonPairedPSCBS.R b/R/segmentByNonPairedPSCBS.R
index 147f600..ea4dc1b 100644
--- a/R/segmentByNonPairedPSCBS.R
+++ b/R/segmentByNonPairedPSCBS.R
@@ -154,7 +154,6 @@ setMethodS3("segmentByNonPairedPSCBS", "default", function(CT, betaT, ..., flavo
if (is.na(tauA) && is.na(tauB)) {
mBAF <- abs(betaT - 1/2);
- findPeaksAndValleys <- .use("findPeaksAndValleys", package="aroma.light");
fitT <- findPeaksAndValleys(mBAF);
type <- NULL; rm(list="type"); # To please 'R CMD check'.
fitT <- subset(fitT, type == "peak");
diff --git a/R/segmentByPairedPSCBS.R b/R/segmentByPairedPSCBS.R
index d90940e..112227d 100644
--- a/R/segmentByPairedPSCBS.R
+++ b/R/segmentByPairedPSCBS.R
@@ -328,7 +328,6 @@ setMethodS3("segmentByPairedPSCBS", "default", function(CT, thetaT=NULL, thetaN=
if (is.null(muN) && !is.null(betaN)) {
verbose && enter(verbose, "Calling genotypes from normal allele B fractions");
verbose && str(verbose, betaN);
- callNaiveGenotypes <- .use("callNaiveGenotypes", package="aroma.light");
muN <- callNaiveGenotypes(betaN, censorAt=c(0,1));
verbose && cat(verbose, "Called genotypes:");
verbose && str(verbose, muN);
@@ -348,7 +347,6 @@ setMethodS3("segmentByPairedPSCBS", "default", function(CT, thetaT=NULL, thetaN=
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (tbn) {
verbose && enter(verbose, "Normalizing betaT using betaN (TumorBoost)");
- normalizeTumorBoost <- .use("normalizeTumorBoost", package="aroma.light");
betaTN <- normalizeTumorBoost(betaT=betaT, betaN=betaN, muN=muN, preserveScale=preserveScale);
verbose && cat(verbose, "Normalized BAFs:");
verbose && str(verbose, betaTN);
@@ -790,7 +788,7 @@ setMethodS3("segmentByPairedPSCBS", "default", function(CT, thetaT=NULL, thetaN=
nbrOfTCNLociKK <- tcnSegments[kk,"tcnNbrOfLoci"];
verbose && cat(verbose, "Number of TCN loci in segment: ", nbrOfTCNLociKK);
- rows <- seq(from=rowStart, length=nbrOfTCNLociKK);
+ rows <- seq(from=rowStart, length.out=nbrOfTCNLociKK);
dataKK <- data[rows,,drop=FALSE];
nbrOfLociKK <- nrow(dataKK);
diff --git a/R/zzz.R b/R/zzz.R
index 032b0e7..8652e60 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,65 +1,25 @@
-# This should ideally be added to 'R.utils' one day, e.g. as import().
-# /HB 2014-06-08
-.use <- function(name=NULL, package, ..., mode="function") {
- # Attach package?
- if (is.null(name)) {
- use(package, ...);
- return(invisible(NULL))
- }
-
- # Retrieve a particular function
- use(package, ..., how="load");
- ns <- getNamespace(package);
- res <- get(name, mode=mode, envir=ns);
-
- invisible(res);
-} # .use()
+.use <- function(name, package, ..., mode = "function") {
+ get(name, mode = mode, envir = getNamespace(package))
+}
.onLoad <- function(libname, pkgname) {
## covr: skip=5
- ns <- getNamespace(pkgname);
- pkg <- Package(pkgname);
+ ns <- getNamespace(pkgname)
+ pkg <- Package(pkgname)
# Assign '.PSCBS' object [since 'PSCBS' is a constructor/Class].
- name <- sprintf(".%s", pkgname);
- assign(name, pkg, envir=ns, inherits=FALSE);
-} # .onLoad()
+ name <- sprintf(".%s", pkgname)
+ assign(name, pkg, envir = ns, inherits = FALSE)
+}
.onAttach <- function(libname, pkgname) {
# Copy some pre-memoized CBS-parameter calculations to the 'R.cache'
# cache. This speeds up the calculation for common CBS use cases.
- .prememoize();
-
- # Inform user if DNAcopy is missing
- if (!isPackageInstalled("DNAcopy")) {
- msg <- "The Bioconductor package 'DNAcopy' is not installed. Please see https://www.bioconductor.org/ on how to install it, or try calling PSCBS::installDNAcopy().";
- hrule <- paste(rep("*", times=getOption("width", 80L)-1L), collapse="");
- packageStartupMessage(sprintf("%s\nNOTE: %s\n%s", hrule, msg, hrule));
- }
+ .prememoize()
# Get '.PSCBS' object [since 'PSCBS' is a constructor/Class].
- name <- sprintf(".%s", pkgname);
- pkg <- get(name, envir=getNamespace(pkgname), inherits=FALSE);
- startupMessage(pkg);
+ name <- sprintf(".%s", pkgname)
+ pkg <- get(name, envir = getNamespace(pkgname), inherits = FALSE)
+ startupMessage(pkg)
}
-
-
-############################################################################
-# HISTORY:
-# 2014-06-08
-# o CLEANUP: Using R.utils::use() instead of require().
-# 2014-02-04
-# o Added .useDNAcopy() to simplify backward compatibility.
-# 2013-10-13
-# o Added .onLoad() that creates Package '.PSCBS' object, which is
-# used in .onAttach(). This is a workaround for not allocating a
-# local Package on in .onAttach(), which then will be garbage
-# collected and finalize():d, which in turn can generate cyclic
-# loading of namespaces in R.oo (< 1.16.0).
-# 2013-09-27
-# o Added .useAromaLight() to simplify backward compatibility.
-# o Added .requirePkg() from the R.rsp package.
-# 2011-07-23
-# o Added a namespace to the package.
-############################################################################
diff --git a/README.md b/README.md
index 7bb165d..7cfde1d 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,7 @@ by adding the following
future::plan("multiprocess")
```
to the beginning of the PSCBS script. Everything else will work the
-same. To reset to non-parallel (synchronously) processing, use
-`future::plan("eager")`.
+same. To reset to non-parallel processing, use `future::plan("sequential")`.
To configure this automatically whenever the package is loaded, see
future vignette '[A Future for R: Controlling Default Future Strategy](https://cran.r-project.org/web/packages/future/vignettes/future-4-startup.html)'.
@@ -31,6 +30,13 @@ source('http://callr.org/install#HenrikBengtsson/PSCBS@develop')
This will install the package from source.
+## Contributions
+
+This Git repository uses the [Git Flow](http://nvie.com/posts/a-successful-git-branching-model/) branching model (the [`git flow`](https://github.com/petervanderdoes/gitflow-avh) extension is useful for this). The [`develop`](https://github.com/HenrikBengtsson/PSCBS/tree/develop) branch contains the latest contributions and other code that will appear in the next release, and the [`master`](https://github.com/HenrikBengtsson/PSCBS) branch contains the code of the latest release, which i [...]
+
+Contributing to this package is easy. Just send a [pull request](https://help.github.com/articles/using-pull-requests/). When you send your PR, make sure `develop` is the destination branch on the [PSCBS repository](https://github.com/HenrikBengtsson/PSCBS). Your PR should pass `R CMD check --as-cran`, which will also be checked by <a href="https://travis-ci.org/HenrikBengtsson/PSCBS">Travis CI</a> and <a href="https://ci.appveyor.com/project/HenrikBengtsson/pscbs">AppVeyor CI</a> whe [...]
+
+
## Software status
| Resource: | CRAN | Travis CI | Appveyor |
diff --git a/appveyor.yml b/appveyor.yml
index 3ac6a36..6b5b12e 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -12,15 +12,18 @@ environment:
_R_CHECK_FORCE_SUGGESTS_: false
matrix:
- - R_VERSION: devel
- R_ARCH: x64
+# - R_VERSION: devel
+# R_ARCH: x64
- - R_VERSION: devel
- R_ARCH: i386
+# - R_VERSION: devel
+# R_ARCH: i386
- R_VERSION: release
R_ARCH: x64
+ - R_VERSION: release
+ R_ARCH: i386
+
# DO NOT CHANGE the "init" and "install" sections below
diff --git a/cran-comments.md b/cran-comments.md
index 5ab29ce..ad63651 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,55 +1,39 @@
-# CRAN submission PSCBS 0.62.0
-on 2015-11-10
+# CRAN submission PSCBS 0.63.0
-I've verified that this submission causes *no* issues for
-any of the 11 reverse (non-recursive) package dependencies
-available on CRAN and Bioconductor.
+on 2017-06-27
+
+I've verified that this submission causes no issues for any of the 11 reverse (recursive) package dependencies available on CRAN and Bioconductor.
Thanks in advance
-## Notes not sent to CRAN
+### R CMD check --as-cran validation
+
The package has been verified using `R CMD check --as-cran` on:
* Platform x86_64-apple-darwin13.4.0 (64-bit) [Travis CI]:
- - R 3.2.4 Revised (2016-03-16)
- - R version 3.3.2 (2016-10-31)
+ - R version 3.3.3 (2017-03-06)
+ - R version 3.4.0 (2017-04-21)
* Platform x86_64-unknown-linux-gnu (64-bit) [Travis CI]:
- - R version 3.2.5 (2016-04-14)
- - R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-11-09 r71641)
+ - R version 3.3.3 (2017-03-06)
+ - R version 3.4.0 (2017-04-21)
+ - R Under development (unstable) (2017-06-27 r72858)
* Platform x86_64-pc-linux-gnu (64-bit):
- - R version 3.1.2 (2014-10-31)
- - R version 3.3.0 (2016-05-03)
- - R version 3.3.2 (2016-10-31)
- - R version 3.3.2 Patched (2016-11-09 r71642)
-
-* Platform x86_64-pc-linux-gnu (64-bit) [r-hub]:
- - R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-10-30 r71610)
+ - R version 3.2.0 (2015-04-16)
+ - R version 3.2.5 (2016-04-14)
+ - R version 3.4.0 (2017-04-21)
* Platform i686-pc-linux-gnu (32-bit):
- - R version 3.3.2 (2016-10-31)
+ - R version 3.4.0 (2017-04-21)
* Platform i386-w64-mingw32 (32-bit) [Appveyor CI]:
- - R Under development (unstable) (2016-11-09 r71642)
+ - R version 3.4.0 (2017-04-21)
* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
- - R version 3.3.2 (2016-10-31)
- - R Under development (unstable) (2016-11-09 r71642)
-
-* Platform x86_64-w64-mingw32 (64-bit) [r-hub]:
- - R version 3.2.5 (2016-04-14) (*)
- - R version 3.3.2 (2016-10-31) (*)
+ - R version 3.4.0 (2017-04-21)
* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
- - R version 3.3.2 (2016-10-31)
- - R Under development (unstable) (2016-11-09 r71642)
-
-
-(*) Gives an error on r-hub for Windows, because R.cache
-tries to set up a cache directory under tempdir(), which
-is currently not availble on r-hub, cf.
-https://github.com/r-hub/rhub/issues/50
+ - R version 3.4.0 (2017-04-21)
+ - R Under development (unstable) (2017-06-26 r72857)
diff --git a/incl/999.missingdocs.txt b/incl/999.missingdocs.txt
index 4a9aa7d..e392469 100644
--- a/incl/999.missingdocs.txt
+++ b/incl/999.missingdocs.txt
@@ -129,3 +129,5 @@ updateMeansC1C2 updateMeansC1C2.PairedPSCBS
encodeCalls encodeCalls.data.frame
callGLAO callGLAO.CBS
unTumorBoost unTumorBoost.PairedPSCBS
+isLocallyPhased
+isLocallyPhased.PSCBS
diff --git a/man/Non-documented_objects.Rd b/man/Non-documented_objects.Rd
index 5984a1b..41d24d1 100644
--- a/man/Non-documented_objects.Rd
+++ b/man/Non-documented_objects.Rd
@@ -309,6 +309,8 @@
\alias{callGLAO.CBS}
\alias{unTumorBoost}
\alias{unTumorBoost.PairedPSCBS}
+\alias{isLocallyPhased}
+\alias{isLocallyPhased.PSCBS}
\description{
This page contains aliases for all "non-documented" objects that
diff --git a/man/NonPairedPSCBS.Rd b/man/NonPairedPSCBS.Rd
index 913ee41..6d50836 100644
--- a/man/NonPairedPSCBS.Rd
+++ b/man/NonPairedPSCBS.Rd
@@ -50,7 +50,7 @@ extends \emph{\link[PSCBS]{PSCBS}}\cr
\bold{Methods inherited from PSCBS}:\cr
-append, as.data.frame, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isSegmentSplitter, normalizeTotalCNs, writeSegments
+append, as.data.frame, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isLocallyPhased, isSegmentSplitter, normalizeTotalCNs, writeSegments
\bold{Methods inherited from AbstractCBS}:\cr
adjustPloidyScale, all.equal, append, as.data.frame, clearCalls, drawChangePoints, drawKnownSegments, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractCNs, extractChromosome, extractChromosomes, extractRegions, extractSegments, extractWIG, getChangePoints, getChromosomeOffsets, getChromosomeRanges, getChromosomes, getLocusData, getLocusSignalNames, getMeanEstimators, getSampleName, getSegmentSizes, getSegmentTrackPrefixes, getSegments, load, mergeThreeSegments, mergeTwo [...]
diff --git a/man/PSCBS.Rd b/man/PSCBS.Rd
index 814441a..4d6b017 100644
--- a/man/PSCBS.Rd
+++ b/man/PSCBS.Rd
@@ -46,6 +46,7 @@ extends \emph{\link[PSCBS]{AbstractCBS}}\cr
\bold{Methods:}\cr
\tabular{rll}{
\tab \code{append} \tab -\cr
+ \tab \code{isLocallyPhased} \tab -\cr
\tab \code{normalizeTotalCNs} \tab -\cr
\tab \code{writeSegments} \tab -\cr
}
diff --git a/man/PairedPSCBS.Rd b/man/PairedPSCBS.Rd
index 41deba2..c62865f 100644
--- a/man/PairedPSCBS.Rd
+++ b/man/PairedPSCBS.Rd
@@ -68,7 +68,7 @@ extends \emph{\link[PSCBS]{PSCBS}}\cr
\bold{Methods inherited from PSCBS}:\cr
-append, as.data.frame, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isSegmentSplitter, normalizeTotalCNs, writeSegments
+append, as.data.frame, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isLocallyPhased, isSegmentSplitter, normalizeTotalCNs, writeSegments
\bold{Methods inherited from AbstractCBS}:\cr
adjustPloidyScale, all.equal, append, as.data.frame, clearCalls, drawChangePoints, drawKnownSegments, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractCNs, extractChromosome, extractChromosomes, extractRegions, extractSegments, extractWIG, getChangePoints, getChromosomeOffsets, getChromosomeRanges, getChromosomes, getLocusData, getLocusSignalNames, getMeanEstimators, getSampleName, getSegmentSizes, getSegmentTrackPrefixes, getSegments, load, mergeThreeSegments, mergeTwo [...]
diff --git a/man/estimateDeltaCN.PairedPSCBS.Rd b/man/estimateDeltaCN.PairedPSCBS.Rd
index 92d6239..598284c 100644
--- a/man/estimateDeltaCN.PairedPSCBS.Rd
+++ b/man/estimateDeltaCN.PairedPSCBS.Rd
@@ -20,12 +20,16 @@
}
\usage{
-\method{estimateDeltaCN}{PairedPSCBS}(fit, scale=1, kappa=estimateKappa(fit), ...)
+\method{estimateDeltaCN}{PairedPSCBS}(fit, scale=1, flavor=c("1-kappa", "delta(mode)"),
+ kappa=estimateKappa(fit), adjust=0.2, quantile=0.95, ...)
}
\arguments{
\item{scale}{A \code{\link[base]{numeric}} scale factor in (0,Inf) used for rescaling
(multiplying) the final estimate with.}
+ \item{flavor}{Specifies which type of estimator should be used.}
+ \item{kappa}{Estimate of background signal (used by the \code{"1-kappa"} method).}
+ \item{adjust, quantile}{Tuning parameters (used by the \code{"delta(mode)"} method).}
\item{...}{Not used.}
}
diff --git a/revdep/README.md b/revdep/README.md
index bdc0632..c872ef2 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -4,31 +4,31 @@
|setting |value |
|:--------|:----------------------------|
-|version |R version 3.3.2 (2016-10-31) |
+|version |R version 3.4.0 (2017-04-21) |
|system |x86_64, linux-gnu |
|ui |X11 |
|language |en |
|collate |en_US.UTF-8 |
-|tz |US/Pacific |
-|date |2016-11-10 |
+|tz |America/Los_Angeles |
+|date |2017-06-27 |
## Packages
|package |* |version |date |source |
|:-----------|:--|:-------|:----------|:--------------|
-|aroma.light | |3.4.0 |2016-10-31 |cran (@3.4.0) |
-|DNAcopy | |1.48.0 |2016-10-31 |cran (@1.48.0) |
-|future | |1.1.1 |2016-10-11 |cran (@1.1.1) |
-|ggplot2 | |2.1.0 |2016-03-01 |CRAN (R 3.3.1) |
-|Hmisc | |4.0-0 |2016-11-01 |cran (@4.0-0) |
-|listenv | |0.6.0 |2015-12-28 |CRAN (R 3.3.1) |
-|matrixStats | |0.51.0 |2016-10-09 |cran (@0.51.0) |
-|PSCBS | |0.61.0 |2016-02-04 |CRAN (R 3.3.1) |
-|R.cache | |0.12.0 |2015-11-12 |CRAN (R 3.3.1) |
+|aroma.light | |3.6.0 |2017-05-18 |cran (@3.6.0) |
+|DNAcopy | |1.50.1 |2017-05-18 |cran (@1.50.1) |
+|future | |1.5.0 |2017-05-26 |cran (@1.5.0) |
+|ggplot2 | |2.2.1 |2016-12-30 |cran (@2.2.1) |
+|Hmisc | |4.0-3 |2017-05-02 |cran (@4.0-3) |
+|listenv | |0.6.0 |2015-12-28 |cran (@0.6.0) |
+|matrixStats | |0.52.2 |2017-04-14 |cran (@0.52.2) |
+|PSCBS | |0.62.0 |2016-11-11 |cran (@0.62.0) |
+|R.cache | |0.12.0 |2015-11-12 |cran (@0.12.0) |
|R.devices | |2.15.1 |2016-11-10 |cran (@2.15.1) |
-|R.methodsS3 | |1.7.1 |2016-02-16 |CRAN (R 3.3.1) |
+|R.methodsS3 | |1.7.1 |2016-02-16 |cran (@1.7.1) |
|R.oo | |1.21.0 |2016-11-01 |cran (@1.21.0) |
-|R.rsp | |0.30.0 |2016-05-15 |CRAN (R 3.3.1) |
+|R.rsp | |0.41.0 |2017-04-16 |cran (@0.41.0) |
|R.utils | |2.5.0 |2016-11-07 |cran (@2.5.0) |
# Check results
@@ -38,16 +38,16 @@
|package |version | errors| warnings| notes|
|:----------------|:-------|------:|--------:|-----:|
|ACNE |0.8.1 | 0| 0| 0|
-|aroma.affymetrix |3.0.0 | 0| 0| 0|
+|aroma.affymetrix |3.1.0 | 0| 0| 0|
|aroma.cn |1.6.1 | 0| 0| 0|
-|aroma.core |3.0.0 | 0| 0| 1|
+|aroma.core |3.1.0 | 0| 0| 1|
|calmate |0.12.1 | 0| 0| 0|
|MPAgenomics |1.1.2 | 0| 0| 2|
|NSA |0.0.32 | 0| 0| 6|
-|PECA |1.10.0 | 0| 0| 1|
-|PureCN |1.2.3 | 0| 0| 1|
-|Repitools |1.20.0 | 0| 0| 2|
-|TIN |1.6.0 | 0| 0| 2|
+|PECA |1.12.0 | 0| 0| 1|
+|PureCN |1.6.3 | 0| 0| 1|
+|Repitools |1.22.0 | 0| 0| 3|
+|TIN |1.8.0 | 0| 0| 2|
## ACNE (0.8.1)
Maintainer: Henrik Bengtsson <henrikb at braju.com>
@@ -55,7 +55,7 @@ Bug reports: https://github.com/HenrikBengtsson/ACNE/issues
0 errors | 0 warnings | 0 notes
-## aroma.affymetrix (3.0.0)
+## aroma.affymetrix (3.1.0)
Maintainer: Henrik Bengtsson <henrikb at braju.com>
Bug reports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues
@@ -67,7 +67,7 @@ Bug reports: https://github.com/HenrikBengtsson/aroma.cn/issues
0 errors | 0 warnings | 0 notes
-## aroma.core (3.0.0)
+## aroma.core (3.1.0)
Maintainer: Henrik Bengtsson <henrikb at braju.com>
Bug reports: https://github.com/HenrikBengtsson/aroma.core/issues
@@ -202,7 +202,7 @@ Rd file 'NSANormalization.Rd':
These lines will be truncated in the PDF manual.
```
-## PECA (1.10.0)
+## PECA (1.12.0)
Maintainer: Tomi Suomi <tomi.suomi at utu.fi>
0 errors | 0 warnings | 1 note
@@ -216,39 +216,23 @@ Rd file 'PECA.Rd':
These lines will be truncated in the PDF manual.
```
-## PureCN (1.2.3)
+## PureCN (1.6.3)
Maintainer: Markus Riester <markus.riester at novartis.com>
0 errors | 0 warnings | 1 note
```
-checking R code for possible problems ... NOTE
-Found the following calls to data() loading into the global environment:
-File ‘PureCN/R/bootstrapResults.R’:
- data(purecn.example.output)
-File ‘PureCN/R/callAlterations.R’:
- data(purecn.example.output)
- data(purecn.example.output)
-File ‘PureCN/R/callLOH.R’:
- data(purecn.example.output)
-File ‘PureCN/R/createCurationFile.R’:
- data(purecn.example.output)
-File ‘PureCN/R/curateResults.R’:
- data(purecn.example.output)
- data(purecn.example.output)
-File ‘PureCN/R/plotAbs.R’:
- data(purecn.example.output)
-File ‘PureCN/R/predictSomatic.R’:
- data(purecn.example.output)
-File ‘PureCN/R/readCurationFile.R’:
- data(purecn.example.output)
-See section ‘Good practice’ in ‘?data’.
+checking installed package size ... NOTE
+ installed size is 5.6Mb
+ sub-directories of 1Mb or more:
+ doc 1.6Mb
+ extdata 2.7Mb
```
-## Repitools (1.20.0)
+## Repitools (1.22.0)
Maintainer: Mark Robinson <mark.robinson at imls.uzh.ch>
-0 errors | 0 warnings | 2 notes
+0 errors | 0 warnings | 3 notes
```
checking R code for possible problems ... NOTE
@@ -296,9 +280,18 @@ Rd file 'writeWig.Rd':
writeWig(rs, seq.len = NULL, design=NULL, sample=20, drop.zero=TRUE, normalize=TRUE, verbose=TRUE)
These lines will be truncated in the PDF manual.
+
+checking compiled code ... NOTE
+File ‘Repitools/libs/Repitools.so’:
+ Found no call to: ‘R_useDynamicSymbols’
+
+It is good practice to register native routines and to disable symbol
+search.
+
+See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
```
-## TIN (1.6.0)
+## TIN (1.8.0)
Maintainer: Bjarne Johannessen <bjajoh at rr-research.no>
0 errors | 0 warnings | 2 notes
diff --git a/revdep/problems.md b/revdep/problems.md
index 0fa19e2..b2a2c15 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -4,31 +4,31 @@
|setting |value |
|:--------|:----------------------------|
-|version |R version 3.3.2 (2016-10-31) |
+|version |R version 3.4.0 (2017-04-21) |
|system |x86_64, linux-gnu |
|ui |X11 |
|language |en |
|collate |en_US.UTF-8 |
-|tz |US/Pacific |
-|date |2016-11-10 |
+|tz |America/Los_Angeles |
+|date |2017-06-27 |
## Packages
|package |* |version |date |source |
|:-----------|:--|:-------|:----------|:--------------|
-|aroma.light | |3.4.0 |2016-10-31 |cran (@3.4.0) |
-|DNAcopy | |1.48.0 |2016-10-31 |cran (@1.48.0) |
-|future | |1.1.1 |2016-10-11 |cran (@1.1.1) |
-|ggplot2 | |2.1.0 |2016-03-01 |CRAN (R 3.3.1) |
-|Hmisc | |4.0-0 |2016-11-01 |cran (@4.0-0) |
-|listenv | |0.6.0 |2015-12-28 |CRAN (R 3.3.1) |
-|matrixStats | |0.51.0 |2016-10-09 |cran (@0.51.0) |
-|PSCBS | |0.61.0 |2016-02-04 |CRAN (R 3.3.1) |
-|R.cache | |0.12.0 |2015-11-12 |CRAN (R 3.3.1) |
+|aroma.light | |3.6.0 |2017-05-18 |cran (@3.6.0) |
+|DNAcopy | |1.50.1 |2017-05-18 |cran (@1.50.1) |
+|future | |1.5.0 |2017-05-26 |cran (@1.5.0) |
+|ggplot2 | |2.2.1 |2016-12-30 |cran (@2.2.1) |
+|Hmisc | |4.0-3 |2017-05-02 |cran (@4.0-3) |
+|listenv | |0.6.0 |2015-12-28 |cran (@0.6.0) |
+|matrixStats | |0.52.2 |2017-04-14 |cran (@0.52.2) |
+|PSCBS | |0.62.0 |2016-11-11 |cran (@0.62.0) |
+|R.cache | |0.12.0 |2015-11-12 |cran (@0.12.0) |
|R.devices | |2.15.1 |2016-11-10 |cran (@2.15.1) |
-|R.methodsS3 | |1.7.1 |2016-02-16 |CRAN (R 3.3.1) |
+|R.methodsS3 | |1.7.1 |2016-02-16 |cran (@1.7.1) |
|R.oo | |1.21.0 |2016-11-01 |cran (@1.21.0) |
-|R.rsp | |0.30.0 |2016-05-15 |CRAN (R 3.3.1) |
+|R.rsp | |0.41.0 |2017-04-16 |cran (@0.41.0) |
|R.utils | |2.5.0 |2016-11-07 |cran (@2.5.0) |
# Check results
diff --git a/revdep/timing.md b/revdep/timing.md
index 5f9b0ed..38b438e 100644
--- a/revdep/timing.md
+++ b/revdep/timing.md
@@ -2,16 +2,16 @@
| |package |version | check_time|
|:--|:----------------|:-------|----------:|
-|9 |PureCN |1.2.3 | 693.1|
-|10 |Repitools |1.20.0 | 476|
-|11 |TIN |1.6.0 | 245.3|
-|2 |aroma.affymetrix |3.0.0 | 224.1|
-|8 |PECA |1.10.0 | 183.5|
-|4 |aroma.core |3.0.0 | 141.8|
-|6 |MPAgenomics |1.1.2 | 92.9|
-|3 |aroma.cn |1.6.1 | 55.3|
-|7 |NSA |0.0.32 | 53.1|
-|5 |calmate |0.12.1 | 51.4|
-|1 |ACNE |0.8.1 | 42|
+|9 |PureCN |1.6.3 | 755.2|
+|10 |Repitools |1.22.0 | 334.9|
+|11 |TIN |1.8.0 | 155.7|
+|2 |aroma.affymetrix |3.1.0 | 125.1|
+|8 |PECA |1.12.0 | 119.8|
+|4 |aroma.core |3.1.0 | 90.9|
+|6 |MPAgenomics |1.1.2 | 48.1|
+|3 |aroma.cn |1.6.1 | 44.8|
+|5 |calmate |0.12.1 | 39.6|
+|7 |NSA |0.0.32 | 39.3|
+|1 |ACNE |0.8.1 | 38.7|
diff --git a/tests/segmentByCBS,futures.R b/tests/segmentByCBS,futures.R
index 332d36c..55cb413 100644
--- a/tests/segmentByCBS,futures.R
+++ b/tests/segmentByCBS,futures.R
@@ -35,19 +35,12 @@ str(knownSegments)
message("*** segmentByCBS() via futures ...")
-message("*** segmentByCBS() via 'lazy' futures without attaching 'future' ...")
-future::plan("lazy")
-print(future::plan)
-fitL <- segmentByCBS(data, seed=0xBEEF, verbose=TRUE)
-print(fitL)
-
message("*** segmentByCBS() via futures with 'future' attached ...")
library("future")
oplan <- plan()
-strategies <- c("eager", "lazy")
-if (supportsMulticore()) strategies <- c(strategies, "multicore")
+strategies <- c("sequential", "multiprocess")
## Test 'future.BatchJobs' futures?
pkg <- "future.BatchJobs"
@@ -64,7 +57,6 @@ for (strategy in strategies) {
fit <- segmentByCBS(data, seed=0xBEEF, verbose=TRUE)
fits[[strategy]] <- fit
stopifnot(all.equal(fit, fits[[1]]))
- stopifnot(all.equal(fit, fitL))
}
diff --git a/tests/segmentByPairedPSCBS,futures.R b/tests/segmentByPairedPSCBS,futures.R
index d4a7438..6187a49 100644
--- a/tests/segmentByPairedPSCBS,futures.R
+++ b/tests/segmentByPairedPSCBS,futures.R
@@ -41,8 +41,7 @@ message("*** segmentByPairedPSCBS() via futures ...")
library("future")
oplan <- plan()
-strategies <- c("eager", "lazy")
-if (supportsMulticore()) strategies <- c(strategies, "multicore")
+strategies <- c("sequential", "multiprocess")
## Test 'future.BatchJobs' futures?
pkg <- "future.BatchJobs"
@@ -75,7 +74,6 @@ for (strategy in strategies) {
plan(strategy)
fit <- segmentByPairedPSCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE)
fits[[strategy]] <- fit
-## FIXME: 2015-12-09
stopifnot(all.equal(fit, fits[[1]]))
}
--
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