jointseg: Joint segmentation of multivariate (copy number) signals

This package implements functions to quickly segment multivariate signals into piecewise constant profiles and 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.

AuthorMorgane Pierre-Jean and Pierre Neuvial
Date of publication2015-10-19 07:08:10
MaintainerMorgane Pierre-Jean <morgane.pierrejean@genopole.cnrs.fr>
LicenseLGPL (>= 2.1)
Version0.7.0

View on R-Forge

Man pages

anotherBkp: Get best candidate change point

binMissingValues: binMissingValues

defaultWeights: Compute default weights for the weighted group fused Lasso

doCBS: Run CBS segmentation

doDynamicProgramming: Run segmentation by dynamic programming

doGFLars: Group fused Lars segmentation

doPSCBS: Run Paired PSCBS segmentation

doPSCN: Run PSCN segmentation (defunct)

doRBS: Run RBS segmentation

estimateSd: Robust standard deviation estimator

getCopyNumberDataByResampling: Generate a copy number profile by resampling input data

getTpFp: Calculate the number of true positives and false positives

getUnivJ: Get the contribution of one dimension to the RSE.

getUnivStat: Get the binary test statistic for one dimension

jointSeg: Joint segmentation of multivariate signals

jointSeg-package: Joint segmentation of multivariate (copy number) signals

leftMultiplyByInvXAtXA: leftMultiplyByInvXAtXA

leftMultiplyByXt: leftMultiplyByXt

mapPositionsBack: mapPositionsBack

modelSelection: Model selection

multiplyXtXBySparse: multiplyXtXBySparse

oneBkp: Get best candidate change point

plotSeg: Plot signal and breakpoints with segment-level signal...

prof: profile time and memory usage of a given R expression

pruneByDP: Exact segmentation of a multivariate signal using dynamic...

PSSeg: Parent-Specific copy number segmentation

randomProfile: Generate a random multi-dimensional profile with breakpoints...

segmentByGFLars: Group fused Lars segmentation (low-level)

segmentByRBS: Recursive Binary Segmentation (low-level)

Functions

anotherBkp Man page
binMissingValues Man page
defaultWeights Man page
doCBS Man page
doDynamicProgramming Man page
doGFLars Man page
doPSCBS Man page
doPSCN Man page
doRBS Man page
estimateSd Man page
getCopyNumberDataByResampling Man page
getTpFp Man page
getUnivJ Man page
getUnivStat Man page
jointseg Man page
jointSeg Man page
jointseg-package Man page
leftMultiplyByInvXAtXA Man page
leftMultiplyByXt Man page
mapPositionsBack Man page
modelSelection Man page
multiplyXtXBySparse Man page
oneBkp Man page
plotSeg Man page
prof Man page
pruneByDP Man page
PSSeg Man page
randomProfile Man page
segmentByGFLars Man page
segmentByRBS Man page

Files

jointseg/DESCRIPTION
jointseg/NAMESPACE
jointseg/NEWS
jointseg/R
jointseg/R/PSSeg.R jointseg/R/anotherBkp.R jointseg/R/binMissingValues.R jointseg/R/defaultWeights.R jointseg/R/doCBS.R jointseg/R/doDynamicProgramming.R jointseg/R/doGFLars.R jointseg/R/doPSCBS.R jointseg/R/doPSCN.R jointseg/R/doRBS.R jointseg/R/estimateSd.R jointseg/R/getCopyNumberDataByResampling.R jointseg/R/getTpFp.R jointseg/R/getUnivJ.R jointseg/R/getUnivStat.R jointseg/R/jointSeg.R jointseg/R/leftMultiplyByInvXAtXA.R jointseg/R/leftMultiplyByXt.R jointseg/R/mapPositionsBack.R jointseg/R/modelSelection.R jointseg/R/multiplyXtXBySparse.R jointseg/R/oneBkp.R jointseg/R/plotSeg.R jointseg/R/prof.R jointseg/R/pruneByDP.R jointseg/R/randomProfile.R jointseg/R/segmentByGFLars.R jointseg/R/segmentByRBS.R
jointseg/build
jointseg/build/partial.rdb
jointseg/build/vignette.rds
jointseg/inst
jointseg/inst/CITATION
jointseg/inst/doc
jointseg/inst/doc/PSSeg.Rnw
jointseg/inst/doc/PSSeg.pdf
jointseg/inst/doc/dataGeneration.Rnw
jointseg/inst/doc/dataGeneration.pdf
jointseg/inst/eval
jointseg/inst/eval/GSE11976
jointseg/inst/eval/GSE11976/00.setup.R
jointseg/inst/eval/GSE11976/01.createDataSets.R
jointseg/inst/eval/GSE11976/02a.RBS+DP.R
jointseg/inst/eval/GSE11976/02c.cghseg.R
jointseg/inst/eval/GSE11976/02d.CBS.R
jointseg/inst/eval/GSE11976/02e.PSCBS.R
jointseg/inst/eval/GSE11976/02f.GFLars.R
jointseg/inst/eval/GSE11976/03.perf.R
jointseg/inst/eval/GSE11976/04.pAUC.R
jointseg/inst/eval/GSE11976/05.pAUCcurves.R
jointseg/inst/eval/GSE11976/06.pAUCtable.R
jointseg/inst/eval/GSE11976/SnrForCaughtAndMissedBkp.R
jointseg/inst/eval/GSE11976/myImagePlot.R
jointseg/inst/eval/GSE29172
jointseg/inst/eval/GSE29172/00.setup.R
jointseg/inst/eval/GSE29172/01.createDataSets.R
jointseg/inst/eval/GSE29172/02a.RBS+DP.R
jointseg/inst/eval/GSE29172/02c.cghseg.R
jointseg/inst/eval/GSE29172/02d.CBS.R
jointseg/inst/eval/GSE29172/02e.PSCBS.R
jointseg/inst/eval/GSE29172/02f.GFLars.R
jointseg/inst/eval/GSE29172/03.perf.R
jointseg/inst/eval/GSE29172/04.pAUC.R
jointseg/inst/eval/GSE29172/05.pAUCcurves.R
jointseg/inst/eval/GSE29172/06.pAUCtable.R
jointseg/inst/eval/GSE29172/SnrForCaughtAndMissedBkp.R
jointseg/inst/eval/GSE29172/myImagePlot.R
jointseg/inst/figures
jointseg/inst/figures/SNR.R
jointseg/inst/figures/cnProfiles.tex
jointseg/inst/figures/copyNumberData.R
jointseg/inst/figures/evalTPFP.R
jointseg/inst/otherMethods
jointseg/inst/otherMethods/ASCAT
jointseg/inst/otherMethods/ASCAT/doASCAT.R
jointseg/inst/otherMethods/ASCAT/downloadASCAT.R
jointseg/inst/otherMethods/ASCAT/predictGG.R
jointseg/inst/otherMethods/ASCAT/runASCAT.R
jointseg/inst/otherMethods/CnaStruct
jointseg/inst/otherMethods/CnaStruct/doCnaStruct.R
jointseg/inst/otherMethods/PELT
jointseg/inst/otherMethods/PELT/doPelt.R
jointseg/inst/otherMethods/PELT/doPelt.Rnw
jointseg/inst/otherMethods/PELT/jointSeg.bib
jointseg/inst/otherMethods/PSCN
jointseg/inst/otherMethods/PSCN/doPSCN.R
jointseg/inst/syntheticProfiles
jointseg/inst/syntheticProfiles/customRegionProba.R
jointseg/inst/syntheticProfiles/firestorm.R
jointseg/inst/syntheticProfiles/sawtooth.R
jointseg/inst/time
jointseg/inst/time/00.setup.R
jointseg/inst/time/R
jointseg/inst/time/R/00.setup.R
jointseg/inst/time/R/01.createDataSets.R
jointseg/inst/time/R/02a.RBS+DP.R
jointseg/inst/time/R/02b.PSCN.R
jointseg/inst/time/R/02c.cghseg.R
jointseg/inst/time/R/02d.CBS.R
jointseg/inst/time/R/02e.PSCBS.R
jointseg/inst/time/R/02f.GFLars.R
jointseg/inst/time/R/02g.CnaStruct.R
jointseg/inst/time/R/02i.DPSeg2d.R
jointseg/inst/time/R/Script.R
jointseg/man
jointseg/man/PSSeg.Rd jointseg/man/anotherBkp.Rd jointseg/man/binMissingValues.Rd jointseg/man/defaultWeights.Rd jointseg/man/doCBS.Rd jointseg/man/doDynamicProgramming.Rd jointseg/man/doGFLars.Rd jointseg/man/doPSCBS.Rd jointseg/man/doPSCN.Rd jointseg/man/doRBS.Rd jointseg/man/estimateSd.Rd jointseg/man/getCopyNumberDataByResampling.Rd jointseg/man/getTpFp.Rd jointseg/man/getUnivJ.Rd jointseg/man/getUnivStat.Rd jointseg/man/jointSeg-package.Rd jointseg/man/jointSeg.Rd jointseg/man/leftMultiplyByInvXAtXA.Rd jointseg/man/leftMultiplyByXt.Rd jointseg/man/mapPositionsBack.Rd jointseg/man/modelSelection.Rd jointseg/man/multiplyXtXBySparse.Rd jointseg/man/oneBkp.Rd jointseg/man/plotSeg.Rd jointseg/man/prof.Rd jointseg/man/pruneByDP.Rd jointseg/man/randomProfile.Rd jointseg/man/segmentByGFLars.Rd jointseg/man/segmentByRBS.Rd
jointseg/vignettes
jointseg/vignettes/Makefile
jointseg/vignettes/PSSeg.Rnw
jointseg/vignettes/PSSeg.tex
jointseg/vignettes/dataGeneration.Rnw
jointseg/vignettes/dataGeneration.tex
jointseg/vignettes/fig
jointseg/vignettes/fig/PSSeg-plotRBS-1.png
jointseg/vignettes/fig/PSSeg-profile-fig-1.png
jointseg/vignettes/fig/PSSeg-regDat-1.png
jointseg/vignettes/fig/datGen-Affy100-1.png
jointseg/vignettes/fig/datGen-Affy100b-1.png
jointseg/vignettes/fig/datGen-Affy50-1.png
jointseg/vignettes/fig/datGen-Affy70-1.png
jointseg/vignettes/fig/datGen-Illu100-1.png
jointseg/vignettes/fig/datGen-Illu100b-1.png
jointseg/vignettes/fig/datGen-Illu50-1.png
jointseg/vignettes/fig/datGen-Illu79-1.png
jointseg/vignettes/jointSeg.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.