Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Version: 0.65.0 [2019-05-04]
NEW FEATURES:
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:
Version: 0.64.0 [2018-08-12]
NEW FEATURES:
PERFORMANCE:
BUG FIXES:
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:
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:
Version: 0.61.0 [2016-02-03]
SIGNIFICANT CHANGES:
NEW FEATURES:
BUG FIXES:
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:
Version: 0.50.0 [2015-10-14]
SIGNIFICANT CHANGES:
Version: 0.45.1 [2015-09-16]
NEW FEATURES:
BUG FIXES:
Version: 0.45.0 [2015-09-11]
SIGNIFICANT CHANGES:
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]
DEPRECATED AND DEFUNCT:
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:
Version: 0.42.1 [2014-05-05]
BUG FIXES:
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:
BUG FIXES:
Version: 0.41.2 [2014-03-28]
NEW FEATURES:
Version: 0.41.1 [2014-03-28]
NEW FEATURES:
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:
Version: 0.40.4 [2014-02-04]
BUG FIXES:
Version: 0.40.3 [2014-01-29]
NEW FEATURES:
Version: 0.40.2 [2013-12-17]
NEW FEATURES:
BUG FIXES:
Version: 0.40.1 [2013-12-09]
DOCUMENTATION:
CODE REFACTORING:
Version: 0.40.0 [2013-12-07]
CODE REFACTORING:
Version: 0.39.8 [2013-12-04]
DOCUMENTATION:
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:
Version: 0.39.6 [2013-11-23]
NEW FEATURES:
Added clearCalls() for AbstractCBS.
Added extractSegmentDataByLocus() for PairedPSCBS.
BUG FIXES:
Version: 0.39.5 [2013-11-15]
NEW FEATURES:
Version: 0.39.4 [2013-11-14]
BUG FIXES:
Version: 0.39.3 [2013-11-05]
NEW FEATURES:
Version: 0.39.2 [2013-10-28]
NEW FEATURES:
Version: 0.39.1 [2013-10-25]
NEW FEATURES:
BUG FIXES:
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:
CODE REFACTORING:
Version: 0.38.5 [2013-10-18]
BUG FIXES:
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:
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:
Version: 0.38.1 [2013-10-08]
NEW FEATURES:
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:
CODE REFACTORING:
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:
Version: 0.36.0 [2013-08-15]
NEW FEATURES:
Version: 0.35.6 [2013-08-01]
CODE REFACTORING:
Version: 0.35.5 [2013-07-19]
NEW FEATURES:
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:
Version: 0.35.2 [2013-05-20]
DOCUMENTATION:
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:
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:
Version: 0.34.8 [2013-04-20]
DEPRECATED AND DEFUNCT:
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:
Version: 0.34.5 [2013-04-09]
NEW FEATURES:
Version: 0.34.4 [2013-04-05]
NEW FEATURES:
Version: 0.34.3 [2013-04-04]
CODE REFACTORING:
Version: 0.34.2 [2013-03-28]
NEW FEATURES:
Version: 0.34.1 [2013-03-21]
NEW FEATURES:
DOCUMENTATION:
CODE REFACTORING:
Version: 0.34.0 [2013-03-19]
NEW FEATURES:
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:
Version: 0.33.2 [2013-03-09]
NEW FEATURES:
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:
Version: 0.33.1 [2013-03-07]
DOCUMENTATION:
SOFTWARE QUALITY:
Version: 0.33.0 [2013-03-05]
NEW FEATURES:
Version: 0.32.6 [2013-03-04]
DOCUMENTATION:
Version: 0.32.5 [2013-02-09]
BUG FIXES:
CODE REFACTORING:
Version: 0.32.4 [2013-02-07]
NEW FEATURES:
Version: 0.32.3 [2013-02-05]
NEW FEATURES:
Version: 0.32.2 [2013-02-01]
NEW FEATURES:
DOCUMENTATION:
CODE REFACTORING:
Version: 0.32.1 [2013-02-01]
BUG FIXES:
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:
Version: 0.29.9 [2012-11-05]
DOCUMENTATION:
CODE REFACTORING:
Version: 0.29.8 [2012-11-04]
CODE REFACTORING:
Version: 0.29.7 [2012-11-03]
CODE REFACTORING:
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:
Version: 0.29.4 [2012-09-23]
NEW FEATURES:
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:
Version: 0.29.0 [2012-09-14]
NEW FEATURES:
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:
Version: 0.28.4 [2012-09-13]
NEW FEATURES:
Version: 0.28.3 [2012-08-30]
CODE REFACTORING:
Version: 0.28.2 [2012-08-20]
BUG FIXES:
Version: 0.28.1 [2012-08-15]
DOCUMENTATION:
Version: 0.28.0 [2012-07-22]
NEW FEATURES:
BUG FIXES:
Version: 0.27.4 [2012-07-22]
NEW FEATURES:
Version: 0.27.3 [2012-07-10]
DOCUMENTATION:
CODE REFACTORING:
Version: 0.27.2 [2012-07-08]
CODE REFACTORING:
Version: 0.27.1 [2012-07-02]
NEW FEATURES:
Version: 0.27.0 [2012-06-24]
DOCUMENTATION:
CODE REFACTORING:
Version: 0.26.1 [2012-06-05]
NEW FEATURES:
Version: 0.26.0 [2012-06-03]
NEW FEATURES:
DOCUMENTATION:
Version: 0.25.3 [2012-06-03]
BUG FIXES:
Version: 0.25.2 [2012-05-30]
NEW FEATURES:
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:
DOCUMENTATION:
BUG FIXES:
Version: 0.25.0 [2012-04-20]
NEW FEATURES:
Version: 0.24.0 [2012-04-20]
NEW FEATURES:
Version: 0.23.2 [2012-04-20]
BUG FIXES:
$<-.data.frame
(*tmp*
, "rho" ..." if some loci had unknown genomic positions.Version: 0.23.1 [2012-04-20]
NEW FEATURES:
DOCUMENTATION:
Version: 0.23.0 [2012-03-20]
DOCUMENTATION:
Version: 0.22.2 [2012-02-29]
BUG FIXES:
Version: 0.22.1 [2012-02-28]
NEW FEATURES:
Version: 0.22.0 [2012-02-27]
NEW FEATURES:
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:
CODE REFACTORING:
Version: 0.19.8 [2012-02-23]
CODE REFACTORING:
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:
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:
Version: 0.19.3 [2012-01-09]
NEW FEATURES:
BUG FIXES:
Version: 0.19.2 [2011-12-29]
Version: 0.19.1 [2011-12-13]
NEW FEATURES:
Version: 0.19.0 [2011-12-12]
NEW FEATURES:
BUG FIXES:
DOCUMENTATION:
Version: 0.18.2 [2011-12-07]
NEW FEATURES:
BUG FIXES:
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:
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:
Version: 0.17.2 [2011-11-22]
NEW FEATURES:
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:
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:
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:
Version: 0.15.4 [2011-10-30]
NEW FEATURES:
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:
BUG FIXES:
Version: 0.15.1 [2011-10-21]
NEW FEATURES:
Version: 0.15.0 [2011-10-20]
NEW FEATURES:
BUG FIXES:
Version: 0.14.3 [2011-10-17]
NEW FEATURES:
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:
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:
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:
CODE REFACTORING:
Version: 0.13.2 [2011-09-30]
NEW FEATURES:
BUG FIXES:
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:
Version: 0.12.2 [2011-08-27]
CODE REFACTORING:
Version: 0.12.1 [2011-08-08]
BUG FIXES:
Version: 0.12.0 [2011-07-23]
BUG FIXES:
CODE REFACTORING:
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:
Version: 0.11.5 [2011-07-10]
BUG FIXES:
CODE REFACTORING:
Version: 0.11.4 [2011-07-07]
NEW FEATURES:
DOCUMENTATION:
BUG FIXES:
Version: 0.11.3 [2011-07-06]
NEW FEATURES:
DOCUMENTATION:
Version: 0.11.2 [2011-07-05]
BUG FIXES:
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:
NEW FEATURES:
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:
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:
Version: 0.9.53 [2011-04-14]
Version: 0.9.52 [2011-04-14]
BUG FIXES:
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:
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:
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:
Version: 0.9.47 [2011-04-08]
NEW FEATURES:
Added estimateTauABBySmallDH()
Added internal weightedQuantile().
DOCUMENTATION:
CODE REFACTORING:
Version: 0.9.46 [2011-04-08]
BUG FIXES:
Version: 0.9.45 [2011-04-05]
BUG FIXES:
Version: 0.9.44 [2011-02-18]
NEW FEATURES:
Version: 0.9.43 [2011-02-06]
BUG FIXES:
Version: 0.9.42 [2011-02-03]
NEW FEATURES:
Version: 0.9.41 [2011-02-02]
SIGNFICANT CHANGES:
NEW FEATURES:
Version: 0.9.40 [2011-01-27]
NEW FEATURES:
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:
BUG FIXES:
Version: 0.9.37 [2011-01-18]
BUG FIXES:
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:
Version: 0.9.34 [2010-12-09]
BUG FIXES:
Version: 0.9.33 [2010-12-07]
NEW FEATURES:
Version: 0.9.32 [2010-12-03]
BUG FIXES:
Version: 0.9.31 [2010-12-02]
NEW FEATURES:
Version: 0.9.30 [2010-12-01]
CODE REFACTORING:
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:
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:
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:
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:
DOCUMENTATION:
BUG FIXES:
Version: 0.9.10 [2010-11-09]
NEW FEATURES:
BUG FIXES:
Version: 0.9.9 [2010-11-05]
BUG FIXES:
Version: 0.9.8 [2010-11-04]
BUG FIXES:
Version: 0.9.7 [2010-11-03]
BUG FIXES:
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:
Version: 0.9.5 [2010-11-01]
NEW FEATURES:
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:
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:
Version: 0.9.1 [2010-10-20]
NEW FEATURES:
Version: 0.9.0 [2010-10-18]
NEW FEATURES:
Version: 0.8.3 [2010-10-18]
NEW FEATURES:
Version: 0.8.2 [2010-10-17]
NEW FEATURES:
Version: 0.8.1 [2010-10-10]
SIGNIFICANT CHANGES:
NEW FEATURES:
Version: 0.8.0 [2010-10-06]
CODE REFACTORING:
Version: 0.7.8 [2010-10-03]
NEW FEATURES:
Version: 0.7.7 [2010-09-26]
NEW FEATURES:
Version: 0.7.6 [2010-09-24]
NEW FEATURES:
Version: 0.7.5 [2010-09-21]
NEW FEATURES:
Version: 0.7.4 [2010-09-18]
NEW FEATURES:
BUG FIXES:
Version: 0.7.3 [2010-09-16]
NEW FEATURES:
CODE REFACTORING:
Version: 0.7.2 [2010-09-15]
NEW FEATURES:
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:
Version: 0.6.3 [2010-09-02]
NEW FEATURES:
Version: 0.6.2 [2010-07-14]
NEW FEATURES:
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:
BUG FIXES:
Previous clean up introduced bugs.
The dynamic library for hrmode() was not loaded.
Version: 0.5.5 [2010-05-05]
CODE REFACTORING:
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:
Version: 0.5.2 [2010-0?-??]
Version: 0.5.1 [2010-03-31]
SIGNIFICANT CHANGES:
Version: 0.5.0 [2010-03-12]