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.

Author
Morgane Pierre-Jean and Pierre Neuvial
Date of publication
2015-10-19 07:08:10
Maintainer
Morgane Pierre-Jean <morgane.pierrejean@genopole.cnrs.fr>
License
LGPL (>= 2.1)
Version
0.7.0

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