News

Package: PSCBS

Version: 0.65.0 [2019-05-04]

NEW FEATURES:

• The PDF report produced by report() for Paired PSCBS results will now provide an esimate of normal contamination together with a disclaimer.

BUG FIXES:

• A sanity check in segmentByPairedPSCBS() could produce an error on "'length(x) = 5 > 1' in coercion to 'logical(1)'" when running with R_CHECK_LENGTH_1_LOGIC2=true. This bug did *not( affect the results of PSCBS.

• Report templates used by report() would produce error "Error in unit(x, default.units) : 'x' and 'units' must have length > 0" if there are too few loci to plot. This would typically happen when reporting on human chromosome 25 results.

DEPRECATED AND DEFUNCT:

• Argument 'preserveScale' of segmentByPairedPSCBS() is now defunct.

Version: 0.64.0 [2018-08-12]

NEW FEATURES:

• Added c() for CBS and PSCBS objects.

PERFORMANCE:

• segmentByCBS() no longer performs garbage collection, which happened indirectly via a system.time() call that does GC by default.

BUG FIXES:

• plotTrack() for CBS objects would produce error "Argument 'Clim' is not a vector: NULL" when the signal type was unknown. Now it will assume (non-logged) copy-number ratios so it can choose a default 'Clim' range.

DEPRECATED AND DEFUNCT:

• Removed bootstrapDHByRegion() which was defunct since 0.44.0 (Feb 2015).

• append(x, y) for CBS and PSCBS objects is deprecated; use c(x, y) instead.

• Usage of argument 'preserveScale' for segmentByPairedPSCBS() is now deprecated and ignored. It's value is now fixed to FALSE, which has been the default since PSCBS 0.50.0 (Oct 2015).

Version: 0.63.0 [2017-06-27]

SIGNIFICANT CHANGES:

• Package now depends on R (>= 3.2.0) and Bioconductor (>= 3.1) packages.

NEW FEATURES:

• estimateDeltaCN() for PairedPSCBS gained argument 'flavor' and new estimator `flavor = "delta(mode)".

• Added isLocallyPhased() for PSCBS.

CODE REFACTORING:

• Now package imports aroma.light instead of only suggesting it.

• Package tests no longer test against the deprecated lazy strategy of future.

Version: 0.62.0 [2016-11-10]

NEW FEATURES:

• Added normalizeTotalCNs() for PSCBS objects.

• 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).

• Added splitters = TRUE as the default for setSegments().

CODE REFACTORING:

• CLEANUP: Minor internal cleanup and restructuring.

Version: 0.61.0 [2016-02-03]

SIGNIFICANT CHANGES:

• Package now requires R (>= 3.1.2) released October 2014, because of its dependency on the listenv package.

NEW FEATURES:

• 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:

• 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: 0.60.0 [2015-11-17]

NEW FEATURES:

• 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").

• 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.

CODE REFACTORING:

• Bump package dependencies.

Version: 0.50.0 [2015-10-14]

SIGNIFICANT CHANGES:

• 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: 0.45.1 [2015-09-16]

NEW FEATURES:

• More informative error messages when append() for CBS or PSCBS fail.

BUG FIXES:

• 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: 0.45.0 [2015-09-11]

SIGNIFICANT CHANGES:

• Package now requires R (>= 3.1.1) released July 2014. This allows us to use BioC (>= 3.0) (October 2014).

NEW FEATURES:

• segmentByCBS() gained argument 'avg'.

• Add writeWIG() for CBS objects.

• pruneByHClust() no longer gives a message about method "ward" is now named "ward.D".

• Added skip = TRUE to report().

BUG FIXES:

• plotTracks() for CBS ignored arguments 'cex', 'col' and 'meanCol' if two or more chromosomes were plotted.

• joinSegments(), resetSegments() and pruneBySdUndo() gave errors for multi- chromosome (>= 2) segmentation results.

• segmentByCBS() would ignore argument 'w' (weights) if more than one chromosome was fitted.

• tileChromosomes() for CBS returned incorrect locus data.

• gapsToSegments(gaps) gave an error if nrow(gaps) == 0 or contained no 'chromosome' column.

• findLargeGaps() could return NULL. Now it always returns a data.frame.

• 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:

• ROBUSTNESS: Package test coverage is 62%.

• ROBUSTNESS: Explicitly importing core R functions.

Version: 0.44.0 [2015-02-22]

• 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:

• CLEANUP: bootstrapDHByRegion() is defunct (was deprecated since 2013).

CODE REFACTORING:

• ROBUSTNESS: Package test coverage is 58%.

• ROBUSTNESS: Forgot to declare some S3 methods in NAMESPACE.

• SPEEDUP: Now using more functions of matrixStats.

Version: 0.43.0 [2014-06-08]

SIGNIFICANT CHANGES:

• 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.

• 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.

CODE REFACTORING:

• Now using use() of R.utils where possible.

• Bumped package dependencies.

Version: 0.42.2 [2014-05-24]

CODE REFACTORING:

• Bumped package dependencies.

Version: 0.42.1 [2014-05-05]

BUG FIXES:

• 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: 0.42.0 [2014-04-25]

CODE REFACTORING:

• Minor speedup (a few percents) by now byte compiling the package by default.

• CLEANUP: Dropped unnecessary usage of '::'.

• Bumped package dependencies.

Version: 0.41.4 [2014-03-30]

NEW FEATURES:

• 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.

• 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.

• As an alternative to argument 'CT', segmentByPairedPSCBS() now accepts arguments 'thetaT' and 'thetaN', in case 'CT' is calculated as CT = 2 * thetaT / thetaN.

Version: 0.41.3 [2014-03-29]

NEW FEATURES:

• 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:

• In rare cases, callROH() could throw "Error in if (is.na(delta)) { : argument is of length zero".

Version: 0.41.2 [2014-03-28]

NEW FEATURES:

• Added argument 'preserveScale' to segmentByPairedPSCBS(), which is passed as is to normalizeTumorBoost() with the default being TRUE corresponding to the previous default behavior.

Version: 0.41.1 [2014-03-28]

NEW FEATURES:

• 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: 0.41.0 [2014-03-26]

NEW FEATURES:

• Now estimateKappaByC1Density() give more informative error messages if it failed to identify modes for estimating the parameter.

• Added argument 'from' to estimateKappaByC1Density().

BUG FIXES:

• updateMeansC1C2() for PairedPSCBS did not handle missing values (=splitters) in the 'c1c2Swap' field.

• 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:

• Bumped package dependencies.

Version: 0.40.4 [2014-02-04]

BUG FIXES:

• 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: 0.40.3 [2014-01-29]

NEW FEATURES:

• 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: 0.40.2 [2013-12-17]

NEW FEATURES:

• 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:

• getChangePoints() for CBS returned empty results.

Version: 0.40.1 [2013-12-09]

DOCUMENTATION:

• The CBS vignette referred to C1 and C2 in one of the code examples.

CODE REFACTORING:

• Bumped package dependencies.

Version: 0.40.0 [2013-12-07]

CODE REFACTORING:

• CLEANUP: No longer a need for an ad-hoc NAMESPACE import.

Version: 0.39.8 [2013-12-04]

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: 0.39.7 [2013-11-27]

NEW FEATURES:

• Added callGLAO() for CBS.

• Added encodeCalls() for 'data.frame' object returned by getLocusData(..., addCalls = TRUE).

CODE REFACTORING:

• Bumped package dependencies.

Version: 0.39.6 [2013-11-23]

NEW FEATURES:

• Added clearCalls() for AbstractCBS.

• Added extractSegmentDataByLocus() for PairedPSCBS.

BUG FIXES:

• estimateDeltaCN() for CBS assumed aroma.light was attached.

Version: 0.39.5 [2013-11-15]

NEW FEATURES:

• Added estimateDeltaCN() for CBS. Added package system test.

Version: 0.39.4 [2013-11-14]

BUG FIXES:

• 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: 0.39.3 [2013-11-05]

NEW FEATURES:

• Added basic implementations of setLocusData() and setSegments() for AbstractCBS.

Version: 0.39.2 [2013-10-28]

NEW FEATURES:

• Now plotTracksManyChromosomes() for PairedPSCBS also supports tracks "c1,c2", "c1", and "c2".

Version: 0.39.1 [2013-10-25]

NEW FEATURES:

• 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:

• The 'rho' signals returned by getLocusData(..., fields = "full") for PairedPSCBS would have values also for homozygote SNPs.

Version: 0.39.0 [2013-10-23]

NEW FEATURES:

• Now all warnings generated by DNAcopy::CNA() are suppressed, including the common one on "array has repeated maploc positions".

• Added getBootstrapLocusSets() for PairedPSCBS. Added a package system test for it.

• Added argument 'subset' to applyByRegion() for PairedPSCBS.

• Added clearBootstrapSummaries() for PairedPSCBS.

• SPEEDUP: Added argument 'cache' to bootstrapSegmentsAndChangepoints(), which caches the results to file if cache = TRUE.

Version: 0.38.6 [2013-10-20]

BUG FIXES:

• 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:

• Internal restructuring on how bootstrapping of segment means is done.

Version: 0.38.5 [2013-10-18]

BUG FIXES:

• The CBS and Paired PSCBS report templates assumed that the 'R.utils' package is attached.

Version: 0.38.4 [2013-10-15]

CODE REFACTORING:

• CLEANUP: Removed a few unnecessary NAMESPACE imports.

• Bumped package dependencies.

Version: 0.38.3 [2013-10-14]

NEW FEATURES:

• 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.

CODE REFACTORING:

• Now the package vignettes are in vignettes/ and not in inst/doc/, which will not be supported by R (>= 3.1.0).

• 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.

• CLEANUP: Now explicitly importing only what is needed in NAMESPACE.

Version: 0.38.2 [2013-10-13]

BUG FIXES:

• While attaching the package, it could cause a cyclic loading of namespaces.

Version: 0.38.1 [2013-10-08]

NEW FEATURES:

• Now getSmoothLocusData() for CBS also returns column 'count' which specifies the number of (finite) loci averaged over in each bin.

DOCUMENTATION:

• Vignette 'Total copy-number segmentation using CBS' would display the same plot as vignette 'Parent-specific copy-number segmentation using Paired PSCBS'.

• Renamed vignette 'Paired PSCBS' to 'Parent-specific copy-number segmentation using Paired PSCBS'.

BUG FIXES:

• 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:

• Bumped package dependencies.

Version: 0.38.0 [2013-09-27]

CODE REFACTORING:

• 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.

• Now PSCBS imports 'R.cache' (used to only suggest it).

Version: 0.37.2 [2013-09-27]

CODE REFACTORING:

• SPEEDUP: Now utilizing 'matrixStats' functions in more places.

• ROBUSTNESS: Further improved how aroma.light is handled for backward compatibility.

• Bumped package dependencies.

Version: 0.37.1 [2013-09-26]

CODE REFACTORING:

• 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".

• CLEANUP: Minor adjustments to some of the internal workarounds for older versions of 'matrixStats' and 'aroma.light'.

BUG FIXES:

• Forgot to import several functions from 'matrixStats'. These went undetected because 'aroma.light' (<= 1.31.5) attaches the 'matrixStats'.

• segmentByPairedPSCBS() assumed 'aroma.light' was attached.

• One of the system tests assumed 'R.utils' was attached.

Version: 0.37.0 [2013-09-21]

BUG FIXES:

• 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).

• callGNL() for PairedPSCBS used non-defined 'verbose' object.

CODE REFACTORING:

• CLEANUP: Package no longer attaches 'R.utils', only imports it.

• ROBUSTNESS: Now package imports only what is needed from 'DNAcopy'.

Version: 0.36.2 [2013-09-18]

DOCUMENTATION:

• Added vignette 'Total copy-number segmentation using CBS'.

• 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().

CODE REFACTORING:

• ROBUSTNESS: Now package imports 'matrixStats' (previously suggested).

• ROBUSTNESS: Now package declares S3 methods in the NAMESPACE.

• ROBUSTNESS: Package vignettes no longer assumes that the 'R.rsp' package is attached.

• ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().

• Bumped package dependencies.

Version: 0.36.1 [2013-09-10]

CODE REFACTORING:

• CLEANUP: Package no longer utilizes ':::'.

Version: 0.36.0 [2013-08-15]

NEW FEATURES:

• Made extractMinorMajorCNs() for PairedPSCBS acknowledge additional fields related to (C1,C2).

Version: 0.35.6 [2013-08-01]

CODE REFACTORING:

• Updated the vignettes to utilize the new R.rsp features.

Version: 0.35.5 [2013-07-19]

NEW FEATURES:

• ROBUSTNESS: Added a sanity check on the estimates of (tauA, tauB) when they are estimated from data in segmentByNonPairedPSCBS().

Version: 0.35.4 [2013-07-11]

CODE REFACTORING:

• 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.

• Bumped package dependencies.

Version: 0.35.3 [2013-05-25]

CODE REFACTORING:

• 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: 0.35.2 [2013-05-20]

DOCUMENTATION:

• CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

Version: 0.35.1 [2013-05-07]

NEW FEATURES:

• Now estimateDeltaCN() for PairedPSCBS adjust for the ploidy if set.

• Added ploidy() and ploidy()<- for AbstractCBS.

• Now tileChromosomes() no longer gives warnings on "max(i): no non-missing arguments to max; returning -Inf".

Version: 0.35.0 [2013-04-23]

NEW FEATURES:

• SPEEDUP: Now bootstrapTCNandDHByRegion() for PairedPSCBS always estimates the default quantiles in addition to any requested ones.

• SPEEDUP: Made bootstrapTCNandDHByRegion() much faster by adding use.names = FALSE to two internal unlist() statements.

BUG FIXES:

• 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: 0.34.9 [2013-04-22]

BUG FIXES:

• 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.

• 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:

• Utilizing new startupMessage() of R.oo.

Version: 0.34.8 [2013-04-20]

DEPRECATED AND DEFUNCT:

• Removed previously deprecated methods for AbstractCBS.

Version: 0.34.7 [2013-04-18]

NEW FEATURES:

• Added more arguments to plotTracks().

• Now drawLevels() and drawConfidenceBands() for CBS and PairedPSCBS also works for multiple chromosomes.

BUG FIXES:

• 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.

• Internal calcStatsForCopyNeutralABs() would give an error if there was exactly two AB segments.

Version: 0.34.6 [2013-04-11]

BUG FIXES:

• plotTracks(fit, callLoci = TRUE) would color loci incorrectly if more than one chromosome are plotted.

Version: 0.34.5 [2013-04-09]

NEW FEATURES:

• Now callROH() gives an informative error if called on a NonPairedPSCBS object.

Version: 0.34.4 [2013-04-05]

NEW FEATURES:

• Added more end-user control to plotTracks().

Version: 0.34.3 [2013-04-04]

CODE REFACTORING:

• Now package builds with both R.rsp (< 0.9.1) and R.rsp (>= 0.9.1).

Version: 0.34.2 [2013-03-28]

NEW FEATURES:

• Now callGainNeutralLoss(), utilizes callCopyNeutral() by default.

Version: 0.34.1 [2013-03-21]

NEW FEATURES:

• Updated the report generator and its RSP templates.

DOCUMENTATION:

• Clarified in the PSCBS vignette that the NTCN caller is under development, experimental.

CODE REFACTORING:

• SPEEDUP: Made dropChangePoints() faster by only updating the segment statistics/means at the very end.

Version: 0.34.0 [2013-03-19]

NEW FEATURES:

• 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: 0.33.4 [2013-03-19]

NEW FEATURES:

• ROBUSTNESS: Now calcStatsForCopyNeutralABs() for PairedPSCBS does a better job in identifying the TCN mode of the AB segments.

• Added argument 'flavor' to findNeutralCopyNumberState() specifying how to identify the main mode of the AB segments.

• VISUALIZATION: Now plotTracks() for PairedPSCBS displays thresholds for calling AB, LOH and and NTCN.

Version: 0.33.3 [2013-03-12]

DOCUMENTATION:

• Documented 'tauA' and 'tauB' in the help for segmentByNonPairedPSCBS().

Version: 0.33.2 [2013-03-09]

NEW FEATURES:

• Added getLocusData() for PairedPSCBS and NonPairedPSCBS.

DOCUMENTATION:

• Updated the vignettes and the report templates to utilize the new ggplot2 themes - ggplot2 no longer gives a warning on using deprecated functions.

• 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.

CODE REFACTORING:

• Added an [email protected] field to the DESCRIPTION.

Version: 0.33.1 [2013-03-07]

DOCUMENTATION:

• Preparing package vignettes for the upcoming R 3.0.0 support for non-Sweave vignettes.

SOFTWARE QUALITY:

• 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:

• 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:

• Updated the help usage section for all static methods.

Version: 0.32.5 [2013-02-09]

BUG FIXES:

• 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:

• Added a VignetteBuilder field to DESCRIPTION.

Version: 0.32.4 [2013-02-07]

NEW FEATURES:

• Improved some verbose outputs of bootstrapTCNandDHByRegion().

Version: 0.32.3 [2013-02-05]

NEW FEATURES:

• Now pruneByHClust() drops any existing segment calls and quantile mean-level estimates.

Version: 0.32.2 [2013-02-01]

NEW FEATURES:

• Added resetSegments() for AbstractCBS, which drops extra segments columns (e.g. bootstrap statistics and calls) except those obtained from the segment algorithm.

DOCUMENTATION:

• Added a paragraph on avgDH = "median" to the PSCBS vignette's 'Experimental' section.

CODE REFACTORING:

• ROBUSTNESS: Now aroma.light is explicitly required in cases where it is needed.

Version: 0.32.1 [2013-02-01]

BUG FIXES:

• 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:

• Added arguments 'avgTCN' and 'avgDH' to segmentByPairedPSCBS().

• 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:

• CLEANUP: Now packages R.methodsS3 and R.oo are only imported.

• CLEANUP: Package no longer explicitly imports digest.

Version: 0.30.0 [2012-11-05]

NEW FEATURES:

• GENERALIZATION: Now bootstrapTCNandDHByRegion() works for more "flavors", e.g the default ('tcn') used by segmentByNonPairedPSCBS().

Version: 0.29.9 [2012-11-05]

DOCUMENTATION:

• FIX: example(segmentByNonPairedPSCBS) was for the paired case.

CODE REFACTORING:

• 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:

• CLEANUP: Replaced all whichVector() with which(), because the latter is now the fastest again.

Version: 0.29.7 [2012-11-03]

CODE REFACTORING:

• Updated deprecated ggplot2 functions in the RSP reports.

Version: 0.29.6 [2012-11-01]

CODE REFACTORING:

• Bumped package dependencies.

• CRAN POLICY: Made the examples run faster for 'R CMD check'.

Version: 0.29.5 [2012-10-16]

BUG FIXES:

• 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:

• 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:

• 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.

• 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).

• ROBUSTNESS: Now append() for CBS and PSCBS drops column 'length' from 'knownSegments', iff it exists.

• Now nbrOfChangePoints() for AbstractCBS calculates only change points of connected neighboring segments.

BUG FIXES:

• seqOfSegmentsByDP() for AbstractCBS would not handle empty segments, which could occur if 'knownSegments' for instance included centromere gaps.

• 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:

• 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.

• REPORT: Now report(fit, ..., rspTags) for AbstractCBS looks for the RSP template named (,),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.

• 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:

• Added argument 'dropMissingCT' to segmentByPairedPSCBS().

Version: 0.29.0 [2012-09-14]

NEW FEATURES:

• Added trial version of pruneByDP() for AbstractCBS.

Version: 0.28.6 [2012-09-13]

NEW FEATURES:

• Now tileChromosomes() also adjusts 'knownSegments'.

• Added argument 'dropGaps' to gapsToSegments().

• Updated all.equal() for AbstractCBS to compare locus-level data, segments, and other fields.

Version: 0.28.5 [2012-09-13]

NEW FEATURES:

• 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:

• 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:

• 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:

• segmentByNonPairedPSCBS() forgot to specify namespace aroma.light when trying to call findPeaksAndValleys().

Version: 0.28.1 [2012-08-15]

DOCUMENTATION:

• Minor grammatical corrections of the Paired PSCBS vignette.

Version: 0.28.0 [2012-07-22]

NEW FEATURES:

• 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:

• 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:

• Now verbose output of segmentByPairedPSCBS() specifies region ranges with greater precision.

Version: 0.27.3 [2012-07-10]

DOCUMENTATION:

• Minor updates to the Paired PSCBS vignettes.

CODE REFACTORING:

• 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:

• Updated package dependencies.

Version: 0.27.1 [2012-07-02]

NEW FEATURES:

• 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:

• Some grammar corrections of the 'Paired PSCBS' vignette.

CODE REFACTORING:

• (An update that should be ignored)

Version: 0.26.1 [2012-06-05]

NEW FEATURES:

• Now segmentByCBS() for data frame:s does a better job identifying the CN signals.

Version: 0.26.0 [2012-06-03]

NEW FEATURES:

• 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:

• 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:

• 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:

• Added writeSegments() for DNAcopy objects.

BUG FIXES:

• as.CNA() for DNAcopy added incorrect chromosome splitters.

• as.CNA() for DNAcopy would ignore argument 'sample' and always return the first sample.

Version: 0.25.1 [2012-05-30]

NEW FEATURES:

• Now callROH() records parameter 'deltaROH' in the results.

DOCUMENTATION:

• Added details to the Paired PSCBS vignette on how to tune the various callers.

BUG FIXES:

• callLOH(..., force = TRUE) would append multiple 'lohCall' columns, if called multiple times.

Version: 0.25.0 [2012-04-20]

NEW FEATURES:

• Added a trial (very much true) version of segmentByNonPairedPSCBS().

Version: 0.24.0 [2012-04-20]

NEW FEATURES:

• 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:

• 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:

• Added RSP report for CBS objects (adopted from ditto for PairedPSCBS).

DOCUMENTATION:

• Updated the 'Paired PSCBS' vignette.

Version: 0.23.0 [2012-03-20]

DOCUMENTATION:

• Added a package vignette.

Version: 0.22.2 [2012-02-29]

BUG FIXES:

• plotTracks(..., add = TRUE) for PairedPSCBS would add TCNs when BAFs and DHs were intended.

Version: 0.22.1 [2012-02-28]

• Updated package dependencies to R.rsp (>= 0.7.3) so that report() for PairedPSCBS no longer require non-public packages.

NEW FEATURES:

• 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:

• Added report() for PairedPSCBS.

Version: 0.21.0 [2012-02-27]

NEW FEATURES:

• Added argument 'fields' to getLocusData() for PairedPSCBS.

• Added renameChromosomes() to AbstractCBS.

Version: 0.20.0 [2012-02-26]

NEW FEATURES:

• Added alpha version of callGainNeutralLoss() for PairedPSCBS, which certainly will be updated in the future. This caller is tested by the system tests.

• Added dropChangePoints() for AbstractCBS.

BUG FIXES:

• extractSegments() for PairedPSCBS would return incorrect row indices, more precisely, overlapping data chunks.

• 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:

• ROBUSTNESS: Added more sanity checks validating the correctness of what is returned by extractSegments() for CBS and PairedPSCBS.

CODE REFACTORING:

• 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:

• ROBUSTNESS: Package now explicitly depends on 'utils'.

Version: 0.19.7 [2012-02-22]

BUG FIXES:

• findLargeGaps() did not handle missing values for argument 'chromosome'.

• segmentByCBS(..., knownSegments = knownSegments) would incorrectly throw a sanity-check exception if 'knownSegments' contains a segment with 'start' and 'stop' positions being equal.

• Argument 'calls' of plotTracks() for PairedPSCBS was ignored if more than one chromosome was plotted.

Version: 0.19.6 [2012-01-24]

NEW FEATURES:

• 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:

• Added details to the help of callLOH() and callAB() on the difference between (AB,LOH) = (TRUE,FALSE) and (AB,LOH) = (TRUE,NA).

• Corrected some of verbose messages of estimateDeltaLOHByMinC1ForNonAB() for PairedPSCBS objects.

Version: 0.19.4 [2012-01-10]

CODE REFACTORING:

• 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:

• 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:

• 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]

• ROBUSTNESS: Explicitly added 'digest' to the list of suggested packages.

Version: 0.19.1 [2011-12-13]

NEW FEATURES:

• Added support for callGainsAndLosses(..., method = "ucsf-dmad") of CBS objects.

Version: 0.19.0 [2011-12-12]

NEW FEATURES:

• Added optional argument 'indices' to getLocusData() to be able to retrieve the locus-level data as indexed by input data.

BUG FIXES:

• 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:

• Clarified in help("segmentByCBS") how missing values are dealt with.

Version: 0.18.2 [2011-12-07]

NEW FEATURES:

• Now plotTracks() for CBS always returns an invisible object.

BUG FIXES:

• pruneBySdUndo() for CBS did not work with more than one array.

Version: 0.18.1 [2011-12-03]

NEW FEATURES:

• Added drawChangePoints() for AbstractCBS.

• Now pruneByHClust() for AbstractCBS updates the segment means.

• Added writeSegments() for PSCBS object.

• Now print() for AbstractCBS returns getSegments(..., simplify = TRUE).

• Added argument 'simplify' to getSegments().

• Added arguments 'name', 'tags' and 'exts' to writeSegments() and writeLocusData() and dropped 'filename'.

Version: 0.18.0 [2011-11-28]

NEW FEATURES:

• Added pruneByHClust() for AbstractCBS, with implementation for CBS and PairedPSCBS.

• extractCNs() for CBS would not return a matrix but a data.frame.

BUG FIXES:

• extractTotalCNs() for CBS would give an error.

Version: 0.17.4 [2011-11-26]

NEW FEATURES:

• Added argument 'updateMeans = TRUE' to callROH() for PairedPSCBS.

• 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.

• 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:

• Added callSegmentationOutliers() and dropSegmentationOutliers() for data frames.

• CLEANUP: Renamed field 'position' of the example data to 'x'. This helps us clean up some of the examples.

BUG FIXES:

• 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:

• Added findLargeGaps() and gapsToSegments().

Version: 0.17.1 [2011-11-21]

BUG FIXES:

• 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.

• resegment() for PairedPSCBS called segmentByCBS() instead of segmentByPairedPSCBS().

Version: 0.17.0 [2011-11-19]

NEW FEATURES:

• 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:

• Added resegment() for CBS and PairedPSCBS for easy resegmentation.

• Adjusted segmentByCBS() such that it can handle 'knownSegments' with chromosome boundaries given as -Inf and +Inf.

• Now argument 'mar' for plotTracks() defaults to NULL.

• ROBUSTNESS: Added redundancy tests for segmentByCBS() and segmentByPairedPSCBS() with argument 'knownSegments'.

• ROBUSTNESS: Now segmentByCBS() does more validation of 'knownSegments'.

• FIX: extractRegions() for AbstractCBS would also show verbose output.

BUG FIXES:

• Now argument/parameter 'seed' is correctly preserved by segmentByCBS(). So is 'tbn' for segmentByPairedPSCBS().

• 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.

• extractSegments() for CBS would throw an error when there were multiple chromosomes.

Version: 0.16.2 [2011-11-16]

NEW FEATURES:

• Now segmentByCBS(..., w) stores weights 'w', if given, in the locus-level data table of the returned CBS object.

• Added pruneBySdUndo() for CBS, which does what undo.splits = "sdundo"' for DNA::segment(), but on the already segmented results.

• Now updateMeans() uses locus-specific weights, iff available.

• Added updateBoundaries() for CBS to update (start,stop) per segment.

• 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:

• Now more segmentation parameters are stored in the CBS object.

• 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().

• Added method = "DNAcopy" to estimateStandardDeviation() for CBS, which estimates the std. dev. using DNAcopy:::trimmed.variance().

BUG FIXES:

• 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:

• Added argument 'oma' and 'mar' to plotTracksManyChromosomes() for PairedPSCBS for setting graphical parameters when 'add' == FALSE.

• Added callROH().

• Added arguments 'from' and 'adjustFor' to updateMeans().

Version: 0.15.5 [2011-11-04]

BUG FIXES:

• extractSegment() for AbstractCBS would give an error, because it called itself instead of extractSegments().

Version: 0.15.4 [2011-10-30]

NEW FEATURES:

• 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:

• callAmplifications() for CBS generated an error, if more than one chromosome were called.

• 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.

• highlightArmCalls() for CBS did not handle empty chromosomes.

• 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:

• Added mergeThreeSegments() to AbstractCBS.

BUG FIXES:

• Recent updates caused segmentByPairedPSCBS(data) not to work when 'data' is a data frame.

Version: 0.15.1 [2011-10-21]

NEW FEATURES:

• 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:

• Added support for specifying priorly known segments, such as chromosome arms and centromeres, in segmentByCBS() via argument 'knownSegments'.

BUG FIXES:

• CLEANUP: Dropped a stray debug output message in segmentByPairedPSCBS().

Version: 0.14.3 [2011-10-17]

NEW FEATURES:

• Added argument 'asMissing' to dropRegions() for AbstractCBS.

Version: 0.14.2 [2011-10-16]

NEW FEATURES:

• Implemented extractCNs() for CBS and PairedPSCBS.

• Added extractTotalCNs() for CBS.

Version: 0.14.1 [2011-10-14]

NEW FEATURES:

• Added implementation of extractRegions() for AbstractCBS, which utilizes extractSegments().

• Added abstract extractSegments() and extractSegment() for AbstractCBS.

• Now extractTCNAndDHs() for PairedPSCBS passes '...' to getSegments().

Version: 0.14.0 [2011-10-10]

CODE REFACTORING:

• CLEANUP: Harmonization of several method names.

• CLEANUP: Internal restructuring of the source code files.

Version: 0.13.5 [2011-10-10]

NEW FEATURES:

• Added dropChangePoint() for AbstractCBS, which is just a "name wrapper" for mergeTwoSegments().

• Added dropRegion() and dropRegions() for AbstractPSCBS, where the former is a wrapper for the latter dropRegions().

• Added updateMeans() and mergeTwoSegments() for CBS in addition already available PairedPSCBS versions.

• Relabeled column 'id' to 'sampleName' returned by getSegments().

BUG FIXES:

• For so called "splitter" rows, not all columns returned by getSegments() of CBS were missing values.

• The object returned by as.CBS() of DNAcopy did not have the correct class hierarchy.

CODE REFACTORING:

• ROBUSTNESS: Now using getSegments() everywhere possible.

Version: 0.13.4 [2011-10-08]

NEW FEATURES:

• Added all.equal() for AbstractCBS, which does not compare attributes.

• Added optional argument 'regions' to getCallStatistics() of CBS in order to calculate call statistics on subsets of chromosomes, e.g. chromosome arms.

• Added drawChromosomes() for CBS.

• Added getCallStatisticsByArms(), callArms() and highlightArmCalls() for CBS objects.

CODE REFACTORING:

• 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:

• 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.

• GENERALIZATION: Now all segmentation result classes (CBS and PSCBS) inherits from the AbstractCBS class, which provides methods such as getSampleName(), getChromosomes() and getSegments().

DOCUMENTATION:

• Added lots of more help pages.

CODE REFACTORING:

• CLEANUP: Dropped empty callSegments() for PairedPSCBS.

Version: 0.13.2 [2011-09-30]

NEW FEATURES:

• GENERALIZATION: Now drawLevels() for PairedPSCBS allows for drawing segmentation results in 'betaT' space.

BUG FIXES:

• plotTracks2(..., panels = "dh") gave an error due to a forgotten assignment.

Version: 0.13.1 [2011-09-06]

NEW FEATURES:

• 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.

• Now segmentByCBS() always returns a CBS object. To coerce to a DNAcopy object (as defined in the DNAcopy class) use as.DNAcopy().

• Added coerce methods as.DNAcopy() for CBS objects and as.CBS() for DNAcopy objects.

Version: 0.13.0 [2011-09-01]

NEW FEATURES:

• GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.

• Added append() for CBS objects.

BUG FIXES:

• 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:

• 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:

• 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:

• 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:

• 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:

• Added a section to help("segmentByPairedPSCBS") on the importance of doing a whole-genome PSCBS segmentations if calling AB and LOH states afterward.

• 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:

• 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:

• 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:

• ROBUSTNESS: Fixed partial argument matchings in arrowsC1C2() and arrowsDeltaC1C2() for PairedPSCBS.

Version: 0.11.4 [2011-07-07]

NEW FEATURES:

• 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:

• Removed obsolete references to the R-forge repository.

BUG FIXES:

• 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:

• 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:

• 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:

• 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:

• Clarified that argument 'CT' should be tumor copy number ratios relative to the normal.

• Added Rd help for as.data.frame() of PairedPSCBS.

Version: 0.11.0 [2011-06-14]

SIGNIFICANT CHANGES:

• 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:

• GENERALIZATION: Added argument 'columnNamesFlavor' to segmentByCBS().

Version: 0.10.2 [2011-06-07]

CODE REFACTORING:

• CLEANUP: Cleaned up the example():s.

• Added more biocViews categories to DESCRIPTION

Version: 0.10.1 [2011-05-31]

NEW FEATURES:

• 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.

• Added installDNAcopy(), which will install DNAcopy from Bioconductor.

CODE REFACTORING:

• ROBUSTNESS: Now all DNAcopy functions are called as DNAcopy::nnn().

Version: 0.10.0 [2011-05-29]

SIGNIFICANT CHANGES:

• Renamed package to PSCBS (from 'psCBS').

• Renamed all arguments, variables, and functions referring to 'tau' to refer to 'delta' reflecting the notation of the Paired PSCBS paper.

• Renamed options, example code and help pages to reflect new package name.

DOCUMENTATION:

• Updated references in help pages.

• Now the paired PSCBS is formally referred to as 'Paired PSCBS'.

Version: 0.9.54 [2011-04-27]

NEW FEATURES:

• Added argument 'maxC' to estimateTauLOHByMinC1ForNonAB().

Version: 0.9.53 [2011-04-14]

• Added argument 'max' to estimateTauAB() and estimateTauLOH().

Version: 0.9.52 [2011-04-14]

BUG FIXES:

• Argument 'minSize' of callAB() and callLOH() had no effect.

Version: 0.9.51 [2011-04-12]

NEW FEATURES:

• Added argument 'minSize' to callAB() and callLOH() for PairedPSCBS.

• 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:

• 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:

• Updated estimateTauABBySmallDH() for PairedPSCBS to use a "symmetric" quantile estimator.

• Added argument 'midpoint' to estimateTauLOHByMinC1AtNonAB().

BUG FIXES:

• The recent callLOH() would not store the LOH calls.

Version: 0.9.48 [2011-04-10]

NEW FEATURES:

• Added callLOH() for PairedPSCBS, which in turn calls auxiliary methods.

• Added estimateTauLOH() for PairedPSCBS, which in turn calls axillary methods.

• Now callAB(..., force = FALSE) skips the caller if allelic-balance calls already exist.

DOCUMENTATION:

• Update the example for segmentByPairedPSCBS to reflect the restructured AB and LOH callers.

Version: 0.9.47 [2011-04-08]

NEW FEATURES:

• Added estimateTauABBySmallDH()

• Added internal weightedQuantile().

DOCUMENTATION:

• Added help pages for more methods.

CODE REFACTORING:

• CLEANUP: Started to restructure the source code files.

Version: 0.9.46 [2011-04-08]

BUG FIXES:

• 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:

• 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:

• Added estimateHighDHQuantileAtAB() for PairedPSCBS.

Version: 0.9.43 [2011-02-06]

BUG FIXES:

• plotTracks2() queried non-existing argument 'tracks'.

Version: 0.9.42 [2011-02-03]

NEW FEATURES:

• Added estimateKappa() for estimating the normal contamination.

Version: 0.9.41 [2011-02-02]

SIGNFICANT CHANGES:

• Updated default for 'tauAB' of callABandHighAI() and callABandLowC1() to be estimated from data using estimateTauAB().

NEW FEATURES:

• Added argument 'tauTCN' to estimateTauAB().

Version: 0.9.40 [2011-01-27]

NEW FEATURES:

• Added argument 'flavor' to estimateTauAB() for estimating the AB threshold using alternative methods.

Version: 0.9.39 [2011-01-19]

NEW FEATURES:

• Added trial version of new plotTracks2(), which will later replace plotTracks(). Currently it only works for single chromosomes.

• Added support functions, e.g. updateMeans().

Version: 0.9.38 [2011-01-18]

NEW FEATURES:

• Added arguments 'changepoints' and 'col' to plotTracks() for PairedPSCBS.

• Now plotTracks(..., add = FALSE) for PairedPSCBS only sets up subplots if argument 'tracks' specifies more than one panel.

DOCUMENTATION:

• Documented more plotTracks() arguments for PairedPSCBS.

BUG FIXES:

• Now plotTracks(..., add = TRUE) for PairedPSCBS plots to the current figure/panel.

Version: 0.9.37 [2011-01-18]

BUG FIXES:

• 'tcnSegRows' and 'dhSegRows' where not updated by extractByRegions() for PairedPSCBS.

Version: 0.9.36 [2011-01-14]

NEW FEATURES:

• Added estimateTauAB() for estimating the tauAB tuning parameter when calling segments in allelic balance. Updated example(segmentByPairedPSCBS) to illustrate how to use it.

• Added extractByRegions() for PairedPSCBS.

Version: 0.9.35 [2011-01-12]

NEW FEATURES:

• 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:

• 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:

• Added callLowC1ByC1() and callABandLowC1().

Version: 0.9.32 [2010-12-03]

BUG FIXES:

• 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:

• Added option "psCBS/sanityChecks/tolerance" for specifying the tolerance of some internal sanity checks.

Version: 0.9.30 [2010-12-01]

CODE REFACTORING:

• 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:

• Argument 'flavor' of segmentByPairedPSCBS() would be ignored if multiple chromosomes were segmented.

• extractByChromosome() for PSCBS would call it self instead of extractByChromosomes().

Version: 0.9.24 [2010-11-28]

BUG FIXES:

• 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:

• 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.

• 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:

• bootstrapTCNandDHByRegion() would incorrectly include non-polymorphic loci in the set of homozygous SNPs during resampling.

• segmentByPairedPSCBS() would not accept missing values in argument 'chromosome'.

Version: 0.9.21 [2010-11-27]

NEW FEATURES:

• Now arguments '...' of segmentByPairedPSCBS() are passed to the two segmentByCBS() calls.

• 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]

NEW FEATURES:

• Added optional argument 'chromosomes' to plotTracks() to plot a subset of all chromosomes.

• Added extractByChromosomes() for PSCBS.

• Now the default confidence intervals for plotTracks() is (0.05,0.95), if existing.

• Now all call functions estimate symmetric bootstrap quantiles for convenience of plotting confidence intervals.

BUG FIXES:

• callABandHighAI() for PairedPSCBS used the old DH-only bootstrap method.

• The statistical sanity checks of the bootstrap estimates would give an error when only single-sided bootstrap confidence interval was calculated.

• 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]

NEW FEATURES:

• ROBUSTNESS: Added more sanity checks to bootstrapTCNandDHByRegion().

• 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:

• bootstrapTCNandDHByRegion() would give an error if there was only one segment.

• 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]

NEW FEATURES:

• Added argument 'calls' to plotTracks() for highlighting called regions.

• Updated callAllelicBalanceByDH() and callExtremeAllelicImbalanceByDH() to utilize bootstrapTCNandDHByRegion().

• ROBUSTNESS: Now drawConfidenceBands() of PairedPSCBS silently does nothing if the requested bootstrap quantiles are available.

BUG FIXES:

• bootstrapTCNandDHByRegion() for PairedPSCBS would not correctly detect if bootstrap results are already available.

Version: 0.9.17 [2010-11-21]

NEW FEATURES:

• Now plotTracks() supports tracks "tcn,c1", "tcn,c2" and "c1,c2" too.

• 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".

• Added argument 'xlim' to plotTracks() making it possible to zoom in.

Version: 0.9.16 [2010-11-21]

NEW FEATURES:

• Now joinSegments = TRUE is the default for segmentByCBS() and segmentByPairedPSCBS().

• Added argument 'quantiles' to plotTracks(), which if specified draws confidence bands previously estimated from bootstrapping.

• Added drawConfidenceBands() for PairedPSCBS.

• Added bootstrapTCNandDHByRegion() for PairedPSCBS.

• Added standalone joinSegments() for CBS results.

• Now segmentByPairedPSCBS() also returns minor and major copy numbers for each segment.

Version: 0.9.15 [2010-11-21]

NEW FEATURES:

• 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.

• 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]

NEW FEATURES:

• Now it is possible to specify the boundaries of the regions to be segmented as known change points via argument 'knownCPs'.

• Added argument 'joinSegments' to segmentByCBS() and segmentByPairedPSCBS() in order to specify if neighboring segments should be joined or not.

• Now segmentByCBS() and segmentByPairedPSCBS() allow for unknown genomic positions as well as missing total CN signals.

Version: 0.9.13 [2010-11-19]

NEW FEATURES:

• Added argument 'joinSegments' to segmentByCBS() in order to specify if neighboring segments should be joined or not.

Version: 0.9.12 [2010-11-19]

NEW FEATURES:

• Added plotTracks() and drawLevels() etc to CBS results.

• Now segmentByCBS() allows for unknown genomic positions.

• Now segmentByCBS() allows for missing signals.

• 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]

NEW FEATURES:

• Now the 'data' object returned by segmentByCBS() contains field 'index' if and only if the loci had to be reorder along the genome.

DOCUMENTATION:

• Added more details, references to papers, and cross links to other functions to the help pages.

BUG FIXES:

• 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]

NEW FEATURES:

• Added argument 'cex = 1' to plotTracks().

BUG FIXES:

• It was not possible to plot BAF tracks with plotTracks().

Version: 0.9.9 [2010-11-05]

BUG FIXES:

• segmentByCBS() tried to pass non-existing argument 'undo.split' to DNAcopy::segment(). It should be 'undo.splits'.

Version: 0.9.8 [2010-11-04]

BUG FIXES:

• 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]

• ROBUSTNESS: Now bootstrapDHByRegion() uses resample() of R.utils.

BUG FIXES:

• bootstrapDHByRegion() did not sample from the correct unit(s) when there was only one DH signal.

Version: 0.9.6 [2010-11-02]

NEW FEATURES:

• Added arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS().

• Added argument 'undo' to segmentByCBS(), which corresponds to undo.splits = "sdundo" and undo.SD = undo, if undo < +Inf.

BUG FIXES:

• Arguments 'alphaTCN' and 'alphaDH' of segmentByPairedPSCBS() were not used when more than one chromosome were segmented.

Version: 0.9.5 [2010-11-01]

NEW FEATURES:

• Added arguments 'alphaAB' and 'alphaHighAI' to callABandHighAI().

BUG FIXES:

• bootstrapDHByRegion() would give an error if only a single quantile was requested.

• 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]

NEW FEATURES:

• Now the default is a 95% confidence interval for calls.

• 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:

• Now bootstrapDHByRegion() for PairedPSCBS handles the rare case when markers with the same positions are split in two different segments.

• 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]

NEW FEATURES:

• Added argument 'ciRange' to callAllelicBalance() and callExtremeAllelicImbalance().

BUG FIXES:

• bootstrapDHByRegion() for PairedPSCBS would bootstrap from the incorrect set of loci when the DH region contained only one locus.

• 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]

BUG FIXES:

• plotTracks() would give "Error: object 'nbrOfLoci' not found' for whole-genome plots.

Version: 0.9.1 [2010-10-20]

NEW FEATURES:

• Now plotTracks() can plot whole-genome data.

Version: 0.9.0 [2010-10-18]

NEW FEATURES:

• Added arguments 'alphaTCN' and 'alphaDH' to segmentByPairedPSCBS() with defaults according to the paper.

Version: 0.8.3 [2010-10-18]

NEW FEATURES:

• Now segmentByPairedPSCBS() can segment multiple chromosomes.

Version: 0.8.2 [2010-10-17]

NEW FEATURES:

• Added argument 'tbn' to segmentByPairedPSCBS() specifying whether TumorBoostNormalization should be applied or not.

Version: 0.8.1 [2010-10-10]

SIGNIFICANT CHANGES:

• The default for segmentByPairedPSCBS() is now to segment TCN on the original scale, not the sqrt().

NEW FEATURES:

• Added plotTracks() for PairedPSCBS.

Version: 0.8.0 [2010-10-06]

CODE REFACTORING:

• CLEAN UP: Removed all old code, native code and help pages.

Version: 0.7.8 [2010-10-03]

NEW FEATURES:

• 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]

NEW FEATURES:

• Now subsetBySegments() and postsegmentTCN() for PairedPSCBS handles multiple chromosomes.

Version: 0.7.6 [2010-09-24]

NEW FEATURES:

• 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]

NEW FEATURES:

• 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]

NEW FEATURES:

• Added argument 'chromosome' to segmentByPairedPSCBS(), which, if given, adds a chromosome column to the data and segmentation results.

BUG FIXES:

• plot() for PairedPSCBS used a non-defined variable.

Version: 0.7.3 [2010-09-16]

NEW FEATURES:

• Added callABandHighAI() for calling paired PSCBS segmentation results.

CODE REFACTORING:

• Added internal bootstrapping functions.

Version: 0.7.2 [2010-09-15]

NEW FEATURES:

• Added more methods for the PSCBS class.

Version: 0.7.1 [2010-09-08]

NEW FEATURES:

• Added more methods for the PSCBS class.

• Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.

Version: 0.7.0 [2010-09-04]

NEW FEATURES:

• 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]

NEW FEATURES:

• Now segmentByCBS() also works if there are no data points.

Version: 0.6.2 [2010-07-14]

NEW FEATURES:

• 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]

NEW FEATURES:

• 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.

• Added low-level segmentByCBS(), which runs CBS segmentation on a single sample and a single chromosome.

• BACKWARD COMPATIBILITY: Now psCNA() returns a list of length 8.

• Reverted psSegment() back to v0.5.6.

Version: 0.6.0 [2010-07-08]

NEW FEATURES:

• Now psSegmentPaired() returns a data frame (no longer a matrix).

• CLEANUP: Created psSegmentPaired() from psSegment().

CODE REFACTORING:

• CLEANUP: Major cleanup, i.e. renaming variables, reordering etc.

• ROBUSTNESS: Replaced all 1:n with seq(length = n) to deal with n == 0.

• ROBUSTNESS: Now all list elements are referenced by name.

• ROBUSTNESS: Now all iterator variables are written as ii, jj etc.

• Using setMethodS3() of R.methodsS3 to define S3 method.

• Dropping NAMESPACE while package is finished. This makes it easier to patch methods etc.

Version: 0.5.6 [2010-07-07]

DOCUMENTATION:

• Added example(psSegment).

BUG FIXES:

• Previous clean up introduced bugs.

• The dynamic library for hrmode() was not loaded.

Version: 0.5.5 [2010-05-05]

CODE REFACTORING:

• CLEAN UP/ROBUSTNESS: Major code clean up.

Version: 0.5.4 [2010-04-30]

CODE REFACTORING:

• Added internal hrmode().

• CLEANUP: Renamed source files to match function names. Only only function per source file.

Version: 0.5.3 [2010-04-22]

SIGNIFICANT CHANGES:

• ABO updated the psCBS algorithm.

Version: 0.5.2 [2010-0?-??]

• ???

Version: 0.5.1 [2010-03-31]

SIGNIFICANT CHANGES:

• Now psSegment(..., matching.reference = TRUE) does TumorBoost normalization on the allele B fractions before segmentation.

Version: 0.5.0 [2010-03-12]

• Added to R-forge repository.

Reference manual