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)

Files in this package

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

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