jointseg: Joint segmentation of multivariate (copy number) signals
Version 0.7.0

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.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("jointseg", repos="http://R-Forge.R-project.org")

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

PSSeg Man page
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 Source code
getUnivStat Man page Source code
jointSeg Man page
jointseg Man page
jointseg-package Man page
leftMultiplyByInvXAtXA Man page
leftMultiplyByXt Man page
mapPositionsBack Man page Source code
modelSelection Man page
multiplyXtXBySparse Man page
oneBkp Man page
plotSeg Man page
prof Man page Source code
pruneByDP Man page
randomProfile Man page
segmentByGFLars Man page
segmentByRBS Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/PSSeg.R
R/anotherBkp.R
R/binMissingValues.R
R/defaultWeights.R
R/doCBS.R
R/doDynamicProgramming.R
R/doGFLars.R
R/doPSCBS.R
R/doPSCN.R
R/doRBS.R
R/estimateSd.R
R/getCopyNumberDataByResampling.R
R/getTpFp.R
R/getUnivJ.R
R/getUnivStat.R
R/jointSeg.R
R/leftMultiplyByInvXAtXA.R
R/leftMultiplyByXt.R
R/mapPositionsBack.R
R/modelSelection.R
R/multiplyXtXBySparse.R
R/oneBkp.R
R/plotSeg.R
R/prof.R
R/pruneByDP.R
R/randomProfile.R
R/segmentByGFLars.R
R/segmentByRBS.R
build
build/partial.rdb
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/PSSeg.Rnw
inst/doc/PSSeg.pdf
inst/doc/dataGeneration.Rnw
inst/doc/dataGeneration.pdf
inst/eval
inst/eval/GSE11976
inst/eval/GSE11976/00.setup.R
inst/eval/GSE11976/01.createDataSets.R
inst/eval/GSE11976/02a.RBS+DP.R
inst/eval/GSE11976/02c.cghseg.R
inst/eval/GSE11976/02d.CBS.R
inst/eval/GSE11976/02e.PSCBS.R
inst/eval/GSE11976/02f.GFLars.R
inst/eval/GSE11976/03.perf.R
inst/eval/GSE11976/04.pAUC.R
inst/eval/GSE11976/05.pAUCcurves.R
inst/eval/GSE11976/06.pAUCtable.R
inst/eval/GSE11976/SnrForCaughtAndMissedBkp.R
inst/eval/GSE11976/myImagePlot.R
inst/eval/GSE29172
inst/eval/GSE29172/00.setup.R
inst/eval/GSE29172/01.createDataSets.R
inst/eval/GSE29172/02a.RBS+DP.R
inst/eval/GSE29172/02c.cghseg.R
inst/eval/GSE29172/02d.CBS.R
inst/eval/GSE29172/02e.PSCBS.R
inst/eval/GSE29172/02f.GFLars.R
inst/eval/GSE29172/03.perf.R
inst/eval/GSE29172/04.pAUC.R
inst/eval/GSE29172/05.pAUCcurves.R
inst/eval/GSE29172/06.pAUCtable.R
inst/eval/GSE29172/SnrForCaughtAndMissedBkp.R
inst/eval/GSE29172/myImagePlot.R
inst/figures
inst/figures/SNR.R
inst/figures/cnProfiles.tex
inst/figures/copyNumberData.R
inst/figures/evalTPFP.R
inst/otherMethods
inst/otherMethods/ASCAT
inst/otherMethods/ASCAT/doASCAT.R
inst/otherMethods/ASCAT/downloadASCAT.R
inst/otherMethods/ASCAT/predictGG.R
inst/otherMethods/ASCAT/runASCAT.R
inst/otherMethods/CnaStruct
inst/otherMethods/CnaStruct/doCnaStruct.R
inst/otherMethods/PELT
inst/otherMethods/PELT/doPelt.R
inst/otherMethods/PELT/doPelt.Rnw
inst/otherMethods/PELT/jointSeg.bib
inst/otherMethods/PSCN
inst/otherMethods/PSCN/doPSCN.R
inst/syntheticProfiles
inst/syntheticProfiles/customRegionProba.R
inst/syntheticProfiles/firestorm.R
inst/syntheticProfiles/sawtooth.R
inst/time
inst/time/00.setup.R
inst/time/R
inst/time/R/00.setup.R
inst/time/R/01.createDataSets.R
inst/time/R/02a.RBS+DP.R
inst/time/R/02b.PSCN.R
inst/time/R/02c.cghseg.R
inst/time/R/02d.CBS.R
inst/time/R/02e.PSCBS.R
inst/time/R/02f.GFLars.R
inst/time/R/02g.CnaStruct.R
inst/time/R/02i.DPSeg2d.R
inst/time/R/Script.R
man
man/PSSeg.Rd
man/anotherBkp.Rd
man/binMissingValues.Rd
man/defaultWeights.Rd
man/doCBS.Rd
man/doDynamicProgramming.Rd
man/doGFLars.Rd
man/doPSCBS.Rd
man/doPSCN.Rd
man/doRBS.Rd
man/estimateSd.Rd
man/getCopyNumberDataByResampling.Rd
man/getTpFp.Rd
man/getUnivJ.Rd
man/getUnivStat.Rd
man/jointSeg-package.Rd
man/jointSeg.Rd
man/leftMultiplyByInvXAtXA.Rd
man/leftMultiplyByXt.Rd
man/mapPositionsBack.Rd
man/modelSelection.Rd
man/multiplyXtXBySparse.Rd
man/oneBkp.Rd
man/plotSeg.Rd
man/prof.Rd
man/pruneByDP.Rd
man/randomProfile.Rd
man/segmentByGFLars.Rd
man/segmentByRBS.Rd
vignettes
vignettes/Makefile
vignettes/PSSeg.Rnw
vignettes/PSSeg.tex
vignettes/dataGeneration.Rnw
vignettes/dataGeneration.tex
vignettes/fig
vignettes/fig/PSSeg-plotRBS-1.png
vignettes/fig/PSSeg-profile-fig-1.png
vignettes/fig/PSSeg-regDat-1.png
vignettes/fig/datGen-Affy100-1.png
vignettes/fig/datGen-Affy100b-1.png
vignettes/fig/datGen-Affy50-1.png
vignettes/fig/datGen-Affy70-1.png
vignettes/fig/datGen-Illu100-1.png
vignettes/fig/datGen-Illu100b-1.png
vignettes/fig/datGen-Illu50-1.png
vignettes/fig/datGen-Illu79-1.png
vignettes/jointSeg.bib
jointseg documentation built on May 21, 2017, 1:13 a.m.