Removed defunct append() for AbtractCBS.
Removed defunct load() and save() for AbtractCBS.
After removing the above functions, library(PSCBS) no longer reports on functions being masked.
wtd.quantile() function. Instead, we have adopted its GPL (>=2) code. The reason for doing so is that Hmisc no longer installs out of the box on platforms, e.g. macOS M1, but also that Hmisc has a large number of package dependencies, which adds an unnecessary installation weight to the PSCBS package for this single function.segmentByCBS() and segmentByPairedPSCBS() would produce warnings on possibly unreliable random numbers due to parallel processing in the case they segmented multiple chromosomes or segments.
Fixed a few partial getSegments() argument name matching (splitter -> splitters).
append(x, y) for CBS and PSCBS objects, deprecated since v0.64.0 is defunct; use c(x, y) instead.
save() for CBS and PSCBS objects and corresponding CBS$load() and PSCBS$load() methods are defunct. We recommend to use base-R functions saveRDS() and readRDS() instead. If backward compatibility with the defunct save() and load() methods, the saveObject() and loadObject() functions from the R.utils package can be used.
report() for Paired PSCBS results will now provide an estimate of normal contamination together with a disclaimer.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.
preserveScale of segmentByPairedPSCBS() is now defunct.c() for CBS and PSCBS objects.segmentByCBS() no longer performs garbage collection, which happened indirectly via a system.time() call that does GC by default.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.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.
Use 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).
estimateDeltaCN() for PairedPSCBS gained argument flavor and new estimator flavor = "delta(mode)".
Added isLocallyPhased() for PSCBS.
Now package imports aroma.light instead of only suggesting it.
Package tests no longer test against the deprecated ‘lazy’ strategy of future.
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().
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).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.
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.append() for CBS or PSCBS fail.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.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().
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 it 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.
ROBUSTNESS: Package test coverage is 62%.
ROBUSTNESS: Explicitly importing core R functions.
bootstrapDHByRegion() is defunct (was deprecated since 2013).ROBUSTNESS: Package test coverage is 58%.
ROBUSTNESS: Forgot to declare some S3 methods in NAMESPACE.
SPEEDUP: Now using more functions of matrixStats.
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 Bioconductor (>= 2.13), which were released April 2013 and are in fact old and it’s recommended to use a more recent version of R.
Now using use() of R.utils where possible.
Bumped package dependencies.
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.Minor speedup (a few percents) by now byte compiling the package by default.
CLEANUP: Dropped unnecessary usage of ::.
Bumped package dependencies.
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.
in max(c(NA_integer_, NA_integer_), na.rm = TRUE) : no non-missing arguments to max; returning -Inf.callROH() could throw Error in if (is.na(delta)) { : argument is of length zero.preserveScale to segmentByPairedPSCBS(), which is passed as is to normalizeTumorBoost() with the default being TRUE corresponding to the previous default behavior.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).Now estimateKappaByC1Density() give more informative error messages if it failed to identify modes for estimating the parameter.
Added argument from to estimateKappaByC1Density().
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 utilize those adjustFor options.
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.segmentByPairedPSCBS() asserts that argument muN is not all NAs. Similarily, if muN is called from betaN the same assertion is done after calling.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.getChangePoints() for CBS returned empty results.dropSegmentationOutliers().Added callGLAO() for CBS.
Added encodeCalls() for data.frame object returned by getLocusData(..., addCalls = TRUE).
Added clearCalls() for AbstractCBS.
Added extractSegmentDataByLocus() for PairedPSCBS.
estimateDeltaCN() for CBS assumed aroma.light was attached.estimateDeltaCN() for CBS. Added package system test.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().setLocusData() and setSegments() for AbstractCBS.plotTracksManyChromosomes() for PairedPSCBS also supports tracks "c1,c2", "c1", and "c2".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.rho signals returned by getLocusData(..., fields = "full") for PairedPSCBS would have values also for homozygote SNPs.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.
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.CLEANUP: Removed a few unnecessary NAMESPACE imports.
Bumped package dependencies.
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.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.
getSmoothLocusData() for CBS also returns column count which specifies the number of (finite) loci averaged over in each bin.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’.
tileChromosomes() for CBS did not set the 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.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).
SPEEDUP: Now utilizing matrixStats functions in more places.
ROBUSTNESS: Further improved how aroma.light is handled for backward compatibility.
Bumped package dependencies.
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.
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.
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.
CLEANUP: Package no longer attaches R.utils, only imports it.
ROBUSTNESS: Now package imports only what is needed from DNAcopy.
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().
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.
:::.extractMinorMajorCNs() for PairedPSCBS acknowledge additional fields related to (C1,C2).segmentByNonPairedPSCBS().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.
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.\usage{} lines are at most 90 characters long.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.
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.
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 Lonnstedt (WEHI) for reporting on this.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.
startupMessage() of R.oo.AbstractCBS.Added more arguments to plotTracks().
Now drawLevels() and drawConfidenceBands() for CBS and PairedPSCBS also works for multiple chromosomes.
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.
plotTracks(fit, callLoci = TRUE) would color loci incorrectly if more than one chromosome are plotted.callROH() gives an informative error if called on a NonPairedPSCBS object.plotTracks().callGainNeutralLoss(), utilizes callCopyNeutral() by default.dropChangePoints() faster by only updating the segment statistics/means at the very end.callCopyNeutralByTCNofAB() for PairedPSCBS calls segments; it is now a bit more conservative in rejecting NTCN.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.
tauA and tauB in the help for segmentByNonPairedPSCBS().getLocusData() for PairedPSCBS and NonPairedPSCBS.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.
Authors@R field to the DESCRIPTION.testROH(). This was done in response to the CRAN farm lowering its precision on some hosts.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)".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.VignetteBuilder field to DESCRIPTION.bootstrapTCNandDHByRegion().pruneByHClust() drops any existing segment calls and quantile mean-level estimates.resetSegments() for AbstractCBS, which drops extra segments columns (e.g. bootstrap statistics and calls) except those obtained from the segment algorithm.avgDH = "median" to the PSCBS vignette’s ‘Experimental’ section.segmentByPairedPSCBS(..., avgDH = "median") only worked for single- chromosome data. Same for avgTCN = "median". Thanks Ritu Roy at UCSF for reporting on this.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.
CLEANUP: Now packages R.methodsS3 and R.oo are only imported.
CLEANUP: Package no longer explicitly imports digest.
bootstrapTCNandDHByRegion() works for more “flavors”, e.g the default ("tcn") used by segmentByNonPairedPSCBS().example(segmentByNonPairedPSCBS) was for the paired case.R CMD check.whichVector() with which(), because the latter is now the fastest again.Bumped package dependencies.
CRAN POLICY: Made the examples run faster for R CMD check.
... 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.plotTracks() [and plotTracksManyChromosomes()] draws segment levels such that it is easier to see them even when they are overlapping.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.
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.
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 <className>(,<rspTags>),report.tex.rsp, where <className> is class(fit)[1] and argument rspTags is an optional comma-separated character string/vector. This makes it possible to have different types of report for the same class of objects.
REPORT: Added argument force to report() for AbstractCBS. This will copy the RSP template files again, although they are already in reports/ output directory.
dropMissingCT to segmentByPairedPSCBS().pruneByDP() for AbstractCBS.Now tileChromosomes() also adjusts knownSegments.
Added argument dropGaps to gapsToSegments().
Updated all.equal() for AbstractCBS to compare locus-level data, segments, and other fields.
segmentByCBS(..., undo = +Inf) returns much faster, which is possible because there is no need to identify new change points.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.weightedMedian(), which used to be in aroma.light.segmentByNonPairedPSCBS() forgot to specify namespace aroma.light when trying to call findPeaksAndValleys().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.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.segmentByPairedPSCBS() specifies region ranges with greater precision.NTCN. The corresponding column in the segmentation results are labeled correspondingly. The Paired PSCBS vignette was updated accordingly.Paired PSCBS vignette.segmentByCBS() for data frame:s does a better job identifying the CN signals.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.all.equal(target, current) for CBS objects would give an error if either target or current had zero segments.writeSegments() for DNAcopy objects.as.CNA() for DNAcopy added incorrect chromosome splitters.
as.CNA() for DNAcopy would ignore argument sample and always return the first sample.
callROH() records parameter deltaROH in the results.callLOH(..., force = TRUE) would append multiple lohCall columns, if called multiple times.segmentByNonPairedPSCBS().segmentByPairedPSCBS(..., flavor = "tcn").segmentByPairedPSCBS() would throw error in $<-.data.frame (*tmp*, "rho" ... if some loci had unknown genomic positions.CBS objects (adopted from ditto for PairedPSCBS).Paired PSCBS vignette.plotTracks(..., add = TRUE) for PairedPSCBS would add TCNs when BAFs and DHs were intended.report() for PairedPSCBS no longer require non-public packages.report(), which can be handy on systems where the default PNG device does not support the alpha channel. Example: setOption("PSCBS::report/useAlphaChannel", FALSE).report() for PairedPSCBS.Added argument fields to getLocusData() for PairedPSCBS.
Added renameChromosomes() to AbstractCBS.
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.
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.
extractSegments() for CBS and PairedPSCBS.PairedPSCBS taken from the aroma.cn package. Some of these may become public later, but for they should be considered internal.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.
getCallStatistics() for CBS asserts that calls have been made. If not, an exception is thrown.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.
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.extractSegments() for PairedPSCBS gives an informative error message that it is not supported if CNs were segmented using flavor "tcn,dh".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.callGainsAndLosses(..., method = "ucsf-dmad") for CBS objects.indices to getLocusData() to be able to retrieve the locus-level data as indexed by input data.gapsToSegments() gave invalid segments for chromosomes with more than one gap. Now gapsToSegments() validates argument gaps and asserts that it returns non-overlapping segments.help("segmentByCBS") how missing values are dealt with.plotTracks() for CBS always returns an invisible object.pruneBySdUndo() for CBS did not work with more than one array.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.
Added pruneByHClust() for AbstractCBS, with implementation for CBS and PairedPSCBS.
extractCNs() for CBS would not return a matrix but a data.frame.
extractTotalCNs() for CBS would give an error.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.
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.
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.findLargeGaps() and gapsToSegments().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().
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.
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.
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.
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().
extractSegments() for CBS would throw an error, because in most cases it would created a corrupt internal segRows field.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().
extractSegment() for AbstractCBS would give an error, because it called itself instead of extractSegments().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.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.
mergeThreeSegments() for AbstractCBS.segmentByPairedPSCBS(data) not to work when data is a data frame.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.segmentByCBS() via argument knownSegments.segmentByPairedPSCBS().asMissing to dropRegions() for AbstractCBS.Implemented extractCNs() for CBS and PairedPSCBS.
Added extractTotalCNs() for CBS.
Added implementation of extractRegions() for AbstractCBS, which utilizes extractSegments().
Added abstract extractSegments() and extractSegment() for AbstractCBS.
Now extractTCNAndDHs() for PairedPSCBS passes ... to getSegments().
CLEANUP: Harmonization of several method names.
CLEANUP: Internal restructuring of the source code files.
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().
For so called “splitter” rows, not all columns returned by getSegments() of CBS were missing values.
The object returned by as.CBS() for DNAcopy did not have the correct class hierarchy.
getSegments() everywhere possible.Added all.equal() for AbstractCBS, which does not compare attributes.
Added optional argument regions to getCallStatistics() for 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.
getChromosomeRanges() of CBS returns a data.frame instead of a matrix, and first column is now chromosome.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().
callSegments() for PairedPSCBS.drawLevels() for PairedPSCBS allows for drawing segmentation results in ‘betaT’ space.plotTracks2(..., panels = "dh") gave an error due to a forgotten assignment.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.
GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.
Added append() for CBS objects.
plotTracksManyChromosomes() and tileChromosomes() for CBS did not work at all and therefore neither plotTracks() for CBS with more than one chromosome.R CMD check is no longer giving a note that the package loads package DNAcopy in .onAttach().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.cat().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.
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.tileChromosomes() for PairedPSCBS was still assuming the old naming convention of column names. This caused plotTracks() to throw an exception when plotting multiple chromosomes.arrowsC1C2() and arrowsDeltaC1C2() for PairedPSCBS.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.callAB(..., force = TRUE) would append additional abCall columns to the segmentation table instead of replacing existing calls.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.chromosome for segmentByPairedPSCBS() did not describe how to segment multiple chromosomes in one call.tcnNbrOfSNPs and tcnNbrOfHets were mistakenly labeled as tcnNbrOr.... Thanks Christine Ho at UC Berkeley for reporting on this.Clarified that argument CT should be tumor copy number ratios relative to the normal.
Added Rd help for as.data.frame() of PairedPSCBS.
columnNamesFlavor to segmentByCBS().CLEANUP: Cleaned up the example():s.
Added more biocViews categories to DESCRIPTION.
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.
DNAcopy::nnn().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.
Updated references in help pages.
Now the paired PSCBS is formally referred to as ‘Paired PSCBS’.
maxC to estimateTauLOHByMinC1ForNonAB().max to estimateTauAB() and estimateTauLOH().minSize of callAB() and callLOH() had no effect.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.
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.Updated estimateTauABBySmallDH() for PairedPSCBS to use a “symmetric” quantile estimator.
Added argument midpoint to estimateTauLOHByMinC1AtNonAB().
callLOH() would not store the LOH calls.Added callLOH() for PairedPSCBS, which in turn calls auxiliary methods.
Added estimateTauLOH() for PairedPSCBS, which in turn calls auxiliary methods.
Now callAB(..., force = FALSE) skips the caller if allelic-balance calls already exist.
segmentByPairedPSCBS() to reflect the restructured AB and LOH callers.Added estimateTauABBySmallDH().
Added internal weightedQuantile().
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.estimateHighDHQuantileAtAB() for PairedPSCBS would throw an error on an undefined trim if verbose output was used.estimateHighDHQuantileAtAB() for PairedPSCBS.plotTracks2() queried non-existing argument tracks.estimateKappa() for estimating the normal contamination.tauAB of callABandHighAI() and callABandLowC1() to be estimated from data using estimateTauAB().tauTCN to estimateTauAB().flavor to estimateTauAB() for estimating the AB threshold using alternative methods.Added trial version of new plotTracks2(), which will later replace plotTracks(). Currently it only works for single chromosomes.
Added support functions, e.g. updateMeans().
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.
plotTracks() arguments for PairedPSCBS.plotTracks(..., add = TRUE) for PairedPSCBS plots to the current figure/panel.tcnSegRows and dhSegRows where not updated by extractByRegions() for PairedPSCBS.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.
postsegmentTCN(..., force = TRUE) for PairedPSCBS also updates the TCN estimates even for segments where the DH segmentation did not find any additional change points.segmentByPairedPSCBS(), then the returned data object would contain betaT identical to betaTN.callLowC1ByC1() and callABandLowC1().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.psCBS/sanityChecks/tolerance for specifying the tolerance of some internal sanity checks.segRows element returned by DNAcopy::segment(). Lots of the code was rewritten and therefore completely new bugs may have been introduced.Argument flavor of segmentByPairedPSCBS() would be ignored if multiple chromosomes were segmented.
extractByChromosome() for PSCBS would call it self instead of extractByChromosomes().
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.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.
bootstrapTCNandDHByRegion() would incorrectly include non-polymorphic loci in the set of homozygous SNPs during resampling.
segmentByPairedPSCBS() would not accept missing values in argument chromosome.
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.
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.
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.
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.
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.
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.
bootstrapTCNandDHByRegion() for PairedPSCBS would not correctly detect if bootstrap results are already available.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.
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.
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.
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.
joinSegments to segmentByCBS() in order to specify if neighboring segments should be joined or not.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.
data object returned by segmentByCBS() contains field index if and only if the loci had to be reorder along the genome.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.cex = 1 to plotTracks().plotTracks().segmentByCBS() tried to pass non-existing argument undo.split to DNAcopy::segment(). It should be undo.splits.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.bootstrapDHByRegion() uses resample() of R.utils.bootstrapDHByRegion() did not sample from the correct unit(s) when there was only one DH signal.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.
alphaTCN and alphaDH of segmentByPairedPSCBS() were not used when more than one chromosome were segmented.alphaAB and alphaHighAI to callABandHighAI().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.
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.
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.
ciRange to callAllelicBalance() and callExtremeAllelicImbalance().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.
plotTracks() would give Error: object 'nbrOfLoci' not found for whole-genome plots.plotTracks() can plot whole-genome data.alphaTCN and alphaDH to segmentByPairedPSCBS() with defaults according to the paper.segmentByPairedPSCBS() can segment multiple chromosomes.tbn to segmentByPairedPSCBS() specifying whether TumorBoostNormalization should be applied or not.segmentByPairedPSCBS() is now to segment TCN on the original scale, not the sqrt().plotTracks() for PairedPSCBS.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.subsetBySegments() and postsegmentTCN() for PairedPSCBS handles multiple chromosomes.postsegmentTCN() for PairedPSCBS, which updates the TCN segment start and ends, estimates and counts given the DH segments.chromosome to segmentByPairedPSCBS(), which, if given, adds a chromosome column to the data and segmentation results.plot() for PairedPSCBS used a non-defined variable.callABandHighAI() for calling paired PSCBS segmentation results.PSCBS class.Added more methods for the PSCBS class.
Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.
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.segmentByCBS() also works if there are no data points.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().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.
Now psSegmentPaired() returns a data frame (no longer a matrix).
CLEANUP: Created psSegmentPaired() from psSegment().
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 methods.
Dropping NAMESPACE while package is finished. This makes it easier to patch methods, etc.
example(psSegment).Previous clean up introduced bugs.
The dynamic library for hrmode() was not loaded.
Added internal hrmode().
CLEANUP: Renamed source files to match function names. Only only function per source file.
psSegment(..., matching.reference = TRUE) does TumorBoost normalization on the allele B fractions before segmentation.