Joint Segmentation of Multivariate (Copy Number) Signals

Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) .


This package implements functions to quickly segment multivariate signals into piecewise-constant profiles, as well as a framework to generate realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies.

Installation

You can install jointseg from github with:

# install.packages("devtools")
devtools::install_github("mpierrejean/jointseg")

Usage

The main high-level joint segmentation functions are:

  • jointSeg for arbitrary signals, see ?jointSeg.
  • PSSeg for bivariate copy-number signals, see ?PSSeg and vignette("PSSeg").

We also refer to vignette("dataGeneration") for a description of the generation of synthetic DNA copy-number profiles using data from the acnr package.

References

Pierre-Jean, M, Rigaill, G. J. and Neuvial, P. (2015). "Performance Evaluation of DNA Copy Number Segmentation Methods." Briefings in Bioinformatics, no. 4: 600–615.

Software status

Resource: GitHub Travis CI Appveyor
Platforms: Multiple Linux & OS X Windows
R CMD check Build status Build status
Test coverage Coverage Status

News

Version 1.0.2 [2019-01-07]

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

Version 1.0.1 [2017-11-28]

  • Bug fixed to pass R CMD check under Solaris

Version 1.0.0 [2017-11-27]

  • CRAN submission.

Version 0.8.2-9000 [2017-11-19]

  • Minor updates to C code.

Version 0.8.1-9000 [2017-07-25]

  • Minor updates to C code to pass R CMD check cleanly under R 3.4.1
  • 'acnr' moved from Depends to Imports

Version 0.8.0-9000 [2017-04-11]

  • Added more tests
  • Fixed Issue #4

Version 0.8.0 [2017-03-22]

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

Version 0.7.4 [2017-03-22]

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

Version 0.7.3 [2016-12-16]

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

Version 0.7.2 [2016-12-15]

  • 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

Version 0.7.1 [2016-11-24]

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

Version 0.7.0 [2015-07-08]

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

Version 0.6.4 [2014-12-19]

  • Bug fixed in vignette (remove GFLars segmentation)

Version 0.6.3 [2014-10-27]

  • Bug fixes for submission to CRAN

Version 0.6.2 [2014-09-09]

  • Updates to vignette.
  • Updates to CITATION.

Version 0.6.1 [2014-07-16]

  • 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.

Version 0.6.0 [2014-06-18]

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

Version 0.5.4 [2014-06-06]

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

Version 0.5.3 [2014-06-04]

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

Version 0.5.2 [2014-05-30]

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

Version 0.5.1 [2014-05-29]

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

Version 0.5.0 [2014-05-26]

  • 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.

Version 0.4.7 [2014-05-14]

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

Version 0.4.6 [2014-05-09]

  • 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.

Version 0.4.5 [2014-05-06]

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

Version 0.4.4 [2014-05-05]

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

Version 0.4.3 [2014-02-20]

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

Version 0.4.2 [2014-02-14]

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

Version 0.4.1 [2014-02-13]

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

Version 0.4.0 [2014-02-13]

  • 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.

Version 0.3.17 [2014-02-12]

  • Updates in 'plotSeg'.

Version 0.3.16 [2013-12-09]

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

Version 0.3.15 [2013-12-06]

  • 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).

Version 0.3.14 [2013-11-29]

  • Added flavor 'DP'.

Version 0.3.13 [2013-11-08]

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

Version 0.3.12 [2013-08-04]

  • 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.

Version 0.3.11 [2013-05-30]

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

Version 0.3.10 [2013-05-16]

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

Version 0.3.9 [2013-04-09]

  • Added argument 'K' to 'pruneByDP'.

Version 0.3.8 [2013-03-27]

  • Modification in 'segmentByCnaStruct'

Version 0.3.7 [2013-03-27]

  • Added segmentation methods PELT and CnaStruct

Version 0.3.6 [2013-03-19]

  • 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'.

Version 0.3.5 [2013-02-26]

  • In 'PSSeg' and 'jointSeg': added argument 'jitter'.
  • In getCopyNumberDataByResampling': added argument 'connex' to forces adjacent regions to be connex.
  • In 'getTprTnr': added argument 'relax'.

Version 0.3.4 [2013-02-18]

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

Version 0.3.3 [2013-02-18]

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

Version 0.3.2 [2013-02-14]

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

Version 0.3.1 [2013-02-07]

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

Version 0.3.0 [2013-01-31]

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

Version 0.2.5 [2013-01-31]

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

Version 0.2.4 [2013-01-25]

  • 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'.

Version 0.2.3 [2013-01-16]

  • 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'.

Version 0.2.2 [2013-01-15]

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

Version 0.2.1 [2013-01-06]

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

Version 0.2.0 [2013-01-03]

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

Version 0.1.21 [2012-12-31]

  • 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'.

Version 0.1.20 [2012-12-30]

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

Version 0.1.19 [2012-12-23]

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

Version 0.1.18 [2012-12-17]

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

Version 0.1.17 [2012-12-15]

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

Version 0.1.16 [2012-12-12]

  • Added 'setNormalContamination'.

Version 0.1.15 [2012-12-07]

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

Version 0.1.14 [2012-12-06]

  • 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.

Version 0.1.13 [2012-12-01]

  • 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.

Version 0.1.12 [2012-11-27]

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

Version 0.1.11 [2012-11-25]

  • Renamed 'randomProfileTCGA' to 'getCopyNumberDataByResampling'.

Version 0.1.10 [2012-11-16]

  • Added 'randomProfileTCGA'.

Version 0.1.9 [2012-10-19]

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

Version 0.1.8 [2012-09-13]

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

Version 0.1.7 [2012-09-13]

  • Some code cleanups.

Version 0.1.6 [2012-08-23]

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

Version 0.1.5 [2012-08-22]

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

Version 0.1.4 [2012-08-21]

  • 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'.

Version 0.1.3 [2012-08-20]

  • 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.

Version 0.1.2 [2012-08-17]

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

Version 0.1.1 [2012-08-15]

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

Version 0.1.0 [2012-08-01]

  • Created.

Reference manual

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install.packages("jointseg")

1.0.2 by Morgane Pierre-Jean, 4 months ago


https://github.com/mpierrejean/jointseg


Report a bug at https://github.com/mpierrejean/jointseg/issues


Browse source code at https://github.com/cran/jointseg


Authors: Morgane Pierre-Jean [aut, cre] , Pierre Neuvial [aut] , Guillem Rigaill [aut]


Documentation:   PDF Manual  


LGPL (>= 2.1) license


Imports acnr, matrixStats, DNAcopy

Suggests PSCBS, R.cache, digest, changepoint, knitr, rmarkdown, testthat


Imported by CNVScope.

Depended on by SegCorr.


See at CRAN