Changes in version 1.0.2 (2019-01-11) - Bug fixed in vignette for CRAN %\VignetteIndexEntry{Generating realistic data} Changes in version 1.0.1 (2017-11-28) - Bug fixed to pass R CMD check under Solaris Changes in version 1.0.0 (2017-11-27) - CRAN submission. Changes in version 0.8.2-9000 - Minor updates to C code. Changes in version 0.8.1-9000 - Minor updates to C code to pass R CMD check cleanly under R 3.4.1 - 'acnr' moved from Depends to Imports Changes in version 0.8.0-9000 - Added more tests - Fixed Issue #4 Changes in version 0.8.0 - Fixed issue #5: the package does not rely on cghseg:::segmeanCO anymore! Changes in version 0.7.4 - Added pruned DPA algorithm [GR] - Added a test that pDPA and classical DP yield identical results for (small) univariate signals Changes in version 0.7.3 - Data generation vignette is now .Rmd instead of .Rnw. Changes in version 0.7.2 - Moved documentation from inlinedocs to roxygen2 (as per Issue #2) - Minor updates to vignette following changes to 'acnr'. - PSSeg vignette is now .Rmd instead of .Rnw Changes in version 0.7.1 - Minor bug fix in 'plotSeg' in the default value of parameter binExclPattern. Changes in version 0.7.0 - In 'PSSeg': added argument 'rankTransform' to allow rank-based segmentation to be performed. Changes in version 0.6.4 - Bug fixed in vignette (remove GFLars segmentation) Changes in version 0.6.3 - Bug fixes for submission to CRAN Changes in version 0.6.2 - Updates to vignette. - Updates to CITATION. Changes in version 0.6.1 - In 'estimateSd': SPEED UP for method "Hall": vectorization. - In 'jointSeg', 'PSseg': it is now possible to run 'modelSelection' on initial segmentation. Default behavior of the functions is unchanged. - In 'getCopyNumberDataByResampling', if 'regAnnot' is NULL (the default), frequencies of regions (0,1), (0,2), (1,1) and (1,2) (the most common alterations) are set to represent 90% of the regions. Changes in version 0.6.0 - Cleanups in DESCRIPTION/NAMESPACE. - Moved 'doCnaStruct' to 'otherMethods/'. - Packages passes R CMD check --as-cran. Changes in version 0.5.4 - Replaced 'jointSeg' by 'jointseg' in 'inst' scripts. Changes in version 0.5.3 - Some changes to the main vignette (now using 'knitr'). - Updates in scripts to perform ASCAT segmentation. Changes in version 0.5.2 - Added a vignette to illustrate how to add a new method. Changes in version 0.5.1 - Changed Illumina to GSE11976 and Affymetrix to GSE29172 - Bug fixed for PSCBS, DynamicProgramming and CBS methods. - Updated scripts Changes in version 0.5.0 - Major changes in the interface of the main functions 'PSSeg' and 'jointseg'. - Now 'doGFLars' is a wrapper calling the lower-level 'segmentByGFLars'. - Now 'doRBS' is a wrapper calling the lower-level 'segmentByRBS'. - Added 'binMissingValues' so that it may be used not only for GFLars. - Cleaned up documentation and examples. Changes in version 0.4.7 - in 'jointSeg': added argument 'segFUN' and flavor "other" to enable a user-defined segmentation method to be used. Changes in version 0.4.6 - BUG FIX in 'doCBS': replaced start bkp given by CBS by end bkp as we consider ends of segments for all methods. Only makes a difference when there are missing values in the signal. Changes in version 0.4.5 - Bug fixed in scripts to build table of the paper. - Updated mapping for d|het segmentations (median). Changes in version 0.4.4 - Added scripts to 'inst/otherMethods' and 'inst/syntheticProfiles' to address referees' comments. Changes in version 0.4.3 - Added 'inst/figures' to reproduce the figures of the paper. Changes in version 0.4.2 - 'plotSeg': Calculation of segment means would fail when a breakpoint was detected between the first and second position. Changes in version 0.4.1 - Renamed function 'jointSeg' to 'jointseg' to avoid name clash with package name. - Now all documented functions are exported. - Updates in vignette. Changes in version 0.4.0 - Added scripts to reproduce methods comparison of the jointSeg paper to dedicated subdirectories. - Added scripts to reproduce figures of the jointSeg paper to 'figures'. - Removed defunct package PSCN from 'Suggests' field, and moved function 'doPSCN' to (newly created) directory 'zzz.defunct'. - Removed 'R.utils' from 'Depends' field. Changes in version 0.3.17 - Updates in 'plotSeg'. Changes in version 0.3.16 - 'segmentByNnn' replaced by 'doNnn'. - Replaced 'segmentByCghseg' by 'doDynamicProgramming'. Changes in version 0.3.15 - Wrappers for PSCN and CnaStruct now operate systematically on log-scaled copy numbers (ie LRRs). Thanks to report by Hugues Sicotte. - Segmentation methods can now be run on numeric vectors or data.frames (when appropriate). Changes in version 0.3.14 - Added flavor 'DP'. Changes in version 0.3.13 - Bumped version number to trigger build by R-forge. Changes in version 0.3.12 - Added function 'getTpFp' so that performance can be evaluated in a scale which does not depend on the signal length. Updated examples and vignette accordingly. Changes in version 0.3.11 - Added argument 'regNames' to 'plotSeg' so that region labels are plotted if available. Changes in version 0.3.10 - Some example code now embedded in 'require()' statements to avoid problems in the R CMD check mechanism of R-forge. Changes in version 0.3.9 - Added argument 'K' to 'pruneByDP'. Changes in version 0.3.8 - Modification in 'segmentByCnaStruct' Changes in version 0.3.7 - Added segmentation methods PELT and CnaStruct Changes in version 0.3.6 - Added flavor "Hall" to estimate standard deviation in 'estimateSd'. - Added argument "DP" in 'PSSeg' and 'jointSeg'. - Added argument "relax" in 'getTprTnr' and definition of true negatives. - Added return value "rse" in 'segmentByRBS'. - Added argument "connex" in 'getCopyNumberByResampling'. Changes in version 0.3.5 - In 'PSSeg' and 'jointSeg': added argument 'jitter'. - In getCopyNumberDataByResampling': added argument 'connex' to forces adjacent regions to be connex. - In 'getTprTnr': added argument 'relax'. Changes in version 0.3.4 - 'segmentByGFLars' now handles missing values. - In 'PSSeg': Flavor "GFLars" can now be run at full resolution Changes in version 0.3.3 - BUG FIX in 'segmentByPSCBS'. - flavor = 'PSBCS' added. - Removed segmentByPairedPSCBS. Changes in version 0.3.2 - BUG FIX in 'modelSelection': if the dimension is too small, in 'jointSeg' if flavor = 'CBS' or 'PSCN' no using of 'modelSelection'. Changes in version 0.3.1 - Bumped acnr dependency (>= 0.1.1) to fix minor case sensitivity issue. - Reduced graphics size in vignette. Changes in version 0.3.0 - Updated vignette. - Passes R CMD check with no errors. Changes in version 0.2.5 - Updated NAMESPACE. - Moved dilution data sets to new package 'acnr'. Changes in version 0.2.4 - Cleanups in doc and return values. - 'jointSeg' now returns 'bestBkp' - Removed 'position' from I/O in 'getCopyNumberDataByResampling' and 'PSSeg'. - In 'plotSeg': added arguments 'exclNames', 'ylabs', and 'binExclPattern' so that 'plotSeg' can handle not only copy number signals. - Improved doc and examples. - Now using 'ERMajustment' for model selection. - BUG FIX in 'segmentByRBS': Empty candidate list would give an error. Now returning early when 'minRegionSize' is too large for 'K'. Changes in version 0.2.3 - Added 'loadCnRegionData'. - Added Affymetrix dilution data set (from GEO:GSE29172 and GSE26302). - Removed 'setNormalContamination' as it is not needed anymore. - In 'getCopyNumberDataByResampling': - Added argument 'regAnnot', through which theoretical frequencies for each CN regions can be specified. - Added arguments 'bkp' and 'regions' to allow for bypassing the breakpoint generation step. - Made the constraints on CN transitions more generic. - Added 'loadCnRegionData'. Changes in version 0.2.2 - Replaced all 'jumps' by 'bkp'. - Added argument 'platform' to 'segmentByPSCN'. - Added Illumina dilution data set (from GEO:GSE11976). Changes in version 0.2.1 - BUG FIX in 'segmentByCghseg': index shift when reshaping results. - Now 'PSSeg' can also run 'CBS' segmentation. Changes in version 0.2.0 - Now 'PSSeg' can also run 'PSCN' and 'cghseg' segmentations. - Updated doc and vignette. Changes in version 0.1.21 - Now 'segmentByRBS' handles missing values. Therefore, 'PSSeg' and 'jointSeg' with the corresponding flavor also do. - Added Argument 'statistic' to 'PSSeg'. - Now 'segmentByRBS' scales each dimension to unit variance using 'estimateSd'. Changes in version 0.1.20 - Some code and doc cleanups. - Renamed 'binSeg' to 'segmentByRBS'. - Renamed 'dpSeg' to 'pruneByDP'. - Renamed 'segmentByGflars' to 'segmentByGFLars'. Changes in version 0.1.19 - SPEEDUP: removed redundant calls to 'getRSE' in 'binSeg'. Changes in version 0.1.18 - Added function 'runPSCN' as a convenient wrapper to PSCN + DP. Changes in version 0.1.17 - Added function 'getTprTnr' to evaluate the performance of segmentation methods. - Added function 'prof' for optional reporting of CPU and memory usage. Changes in version 0.1.16 - Added 'setNormalContamination'. Changes in version 0.1.15 - BUG FIX in 'binSeg': index shift in correspondence b/w breakpoint position and interval. Changes in version 0.1.14 - Added 'binSeg' for binary segmentation. - Added wrappers 'jointSeg', 'plotSeg', 'PSGFL'. - Added argument 'flavor' to 'jointSeg' so that one can run GFLARS or binary segmentation before dynamic programming. Changes in version 0.1.13 - Added example data files and scripts based on public data set GSE19539. - Added scripts to generate these data files from raw CEL files in GSE19539. Changes in version 0.1.12 - Added model selection part to 'modelSelection'. - Removed model selection part in 'dpseg'. Changes in version 0.1.11 - Renamed 'randomProfileTCGA' to 'getCopyNumberDataByResampling'. Changes in version 0.1.10 - Added 'randomProfileTCGA'. Changes in version 0.1.9 - BUG FIX in randomProfile: 'minLength' would not work as expected. Changes in version 0.1.8 - Tentative bug fix in gflars: indices in gammaTemp. - SPEEDUP: removed unnecessary calls to 'complex'. - Updated documentation Changes in version 0.1.7 - Some code cleanups. Changes in version 0.1.6 - SPEEDUP: removed explicit calls to 'matrix()' and 'apply(..., rev)'. - Package documentation now done using 'inlinedocs'. Changes in version 0.1.5 - Improved scripts for assessing replication of the MATLAB version. - Improved scripts for testing speed. Changes in version 0.1.4 - BUG FIX: in optimizeLARS.R, the index in 'lambda' was off by 1. - Added 'value' to the return values of 'optimizeLARS'. - Renamed 'optimizeLARS' to 'gflars'. Changes in version 0.1.3 - BUG FIX: in optimizeLARS.R, 'Y' should be centered but not scaled. - Added dpseg.R: finds the best set of change points from a(n over-) segmentation using joint dynamic programming. Changes in version 0.1.2 - SPEEDUP: replaced 'apply(, 1, sum)' by 'rowSums()'. Changes in version 0.1.1 - Added test scripts for replicating MATLAB version. - Added test scripts for speed trials. Changes in version 0.1.0 - Created.