NEWS

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jointseg 1.0.2 (2019-01-11)

• Bug fixed in vignette for CRAN %\VignetteIndexEntry{Generating realistic data}

jointseg 1.0.1 (2017-11-28)

• Bug fixed to pass R CMD check under Solaris

jointseg 1.0.0 (2017-11-27)

• CRAN submission.

jointseg 0.8.2-9000

• Minor updates to C code.

jointseg 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

jointseg 0.8.0-9000

• Added more tests
• Fixed Issue #4

jointseg 0.8.0

• Fixed issue #5: the package does not rely on cghseg:::segmeanCO anymore!

jointseg 0.7.4

• Added pruned DPA algorithm [GR]
• Added a test that pDPA and classical DP yield identical results for (small) univariate signals

jointseg 0.7.3

• Data generation vignette is now .Rmd instead of .Rnw.

jointseg 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

jointseg 0.7.1

• Minor bug fix in 'plotSeg' in the default value of parameter binExclPattern.

jointseg 0.7.0

• In 'PSSeg': added argument 'rankTransform' to allow rank-based segmentation to be performed.

jointseg 0.6.4

• Bug fixed in vignette (remove GFLars segmentation)

jointseg 0.6.3

• Bug fixes for submission to CRAN

jointseg 0.6.2

• Updates to vignette.
• Updates to CITATION.

jointseg 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.

jointseg 0.6.0

• Cleanups in DESCRIPTION/NAMESPACE.
• Moved 'doCnaStruct' to 'otherMethods/'.
• Packages passes R CMD check --as-cran.

jointseg 0.5.4

• Replaced 'jointSeg' by 'jointseg' in 'inst' scripts.

jointseg 0.5.3

• Some changes to the main vignette (now using 'knitr').
• Updates in scripts to perform ASCAT segmentation.

jointseg 0.5.2

• Added a vignette to illustrate how to add a new method.

jointseg 0.5.1

• Changed Illumina to GSE11976 and Affymetrix to GSE29172
• Bug fixed for PSCBS, DynamicProgramming and CBS methods.
• Updated scripts

jointseg 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.

jointseg 0.4.7

• in 'jointSeg': added argument 'segFUN' and flavor "other" to enable a user-defined segmentation method to be used.

jointseg 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.

jointseg 0.4.5

• Bug fixed in scripts to build table of the paper.
• Updated mapping for d|het segmentations (median).

jointseg 0.4.4

• Added scripts to 'inst/otherMethods' and 'inst/syntheticProfiles' to address referees' comments.

jointseg 0.4.3

• Added 'inst/figures' to reproduce the figures of the paper.

jointseg 0.4.2

• 'plotSeg': Calculation of segment means would fail when a breakpoint was detected between the first and second position.

jointseg 0.4.1

• Renamed function 'jointSeg' to 'jointseg' to avoid name clash with package name.
• Now all documented functions are exported.
• Updates in vignette.

jointseg 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.

jointseg 0.3.17

• Updates in 'plotSeg'.

jointseg 0.3.16

• 'segmentByNnn' replaced by 'doNnn'.
• Replaced 'segmentByCghseg' by 'doDynamicProgramming'.

jointseg 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).

jointseg 0.3.14

• Added flavor 'DP'.

jointseg 0.3.13

• Bumped version number to trigger build by R-forge.

jointseg 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.

jointseg 0.3.11

• Added argument 'regNames' to 'plotSeg' so that region labels are plotted if available.

jointseg 0.3.10

• Some example code now embedded in 'require()' statements to avoid problems in the R CMD check mechanism of R-forge.

jointseg 0.3.9

• Added argument 'K' to 'pruneByDP'.

jointseg 0.3.8

• Modification in 'segmentByCnaStruct'

jointseg 0.3.7

• Added segmentation methods PELT and CnaStruct

jointseg 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'.

jointseg 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'.

jointseg 0.3.4

• 'segmentByGFLars' now handles missing values.
• In 'PSSeg': Flavor "GFLars" can now be run at full resolution

jointseg 0.3.3

• BUG FIX in 'segmentByPSCBS'.
• flavor = 'PSBCS' added.
• Removed segmentByPairedPSCBS.

jointseg 0.3.2

• BUG FIX in 'modelSelection': if the dimension is too small, in 'jointSeg' if flavor = 'CBS' or 'PSCN' no using of 'modelSelection'.

jointseg 0.3.1

• Bumped acnr dependency (>= 0.1.1) to fix minor case sensitivity issue.
• Reduced graphics size in vignette.

jointseg 0.3.0

• Updated vignette.
• Passes R CMD check with no errors.

jointseg 0.2.5

• Updated NAMESPACE.
• Moved dilution data sets to new package 'acnr'.

jointseg 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'.

jointseg 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'.

jointseg 0.2.2

• Replaced all 'jumps' by 'bkp'.
• Added argument 'platform' to 'segmentByPSCN'.
• Added Illumina dilution data set (from GEO:GSE11976).

jointseg 0.2.1

• BUG FIX in 'segmentByCghseg': index shift when reshaping results.
• Now 'PSSeg' can also run 'CBS' segmentation.

jointseg 0.2.0

• Now 'PSSeg' can also run 'PSCN' and 'cghseg' segmentations.
• Updated doc and vignette.

jointseg 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'.

jointseg 0.1.20

• Some code and doc cleanups.
• Renamed 'binSeg' to 'segmentByRBS'.
• Renamed 'dpSeg' to 'pruneByDP'.
• Renamed 'segmentByGflars' to 'segmentByGFLars'.

jointseg 0.1.19

• SPEEDUP: removed redundant calls to 'getRSE' in 'binSeg'.

jointseg 0.1.18

• Added function 'runPSCN' as a convenient wrapper to PSCN + DP.

jointseg 0.1.17

• Added function 'getTprTnr' to evaluate the performance of segmentation methods.
• Added function 'prof' for optional reporting of CPU and memory usage.

jointseg 0.1.16

• Added 'setNormalContamination'.

jointseg 0.1.15

• BUG FIX in 'binSeg': index shift in correspondence b/w breakpoint position and interval.

jointseg 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.

jointseg 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.

jointseg 0.1.12

• Added model selection part to 'modelSelection'.
• Removed model selection part in 'dpseg'.

jointseg 0.1.11

• Renamed 'randomProfileTCGA' to 'getCopyNumberDataByResampling'.

jointseg 0.1.10

• Added 'randomProfileTCGA'.

jointseg 0.1.9

• BUG FIX in randomProfile: 'minLength' would not work as expected.

jointseg 0.1.8

• Tentative bug fix in gflars: indices in gammaTemp.
• SPEEDUP: removed unnecessary calls to 'complex'.
• Updated documentation

jointseg 0.1.7

• Some code cleanups.

jointseg 0.1.6

• SPEEDUP: removed explicit calls to 'matrix()' and 'apply(..., rev)'.
• Package documentation now done using 'inlinedocs'.

jointseg 0.1.5

• Improved scripts for assessing replication of the MATLAB version.
• Improved scripts for testing speed.

jointseg 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'.

jointseg 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.

jointseg 0.1.2

• SPEEDUP: replaced 'apply(, 1, sum)' by 'rowSums()'.

jointseg 0.1.1

• Added test scripts for replicating MATLAB version.
• Added test scripts for speed trials.

jointseg 0.1.0

• Created.