Joint segmentation of multivariate (copy number) signals


[Up] [Top]

Documentation for package ‘jointSeg’ version 0.4.3

Help Pages

jointSeg-package Joint segmentation of multivariate (copy number) signals
doCBS Run CBS segmentation
doCnaStruct # Run cnaStruct segmentation
doDynamicProgramming Run cghseg segmentation
doGFLars Solve the group fused Lasso optimization problem using group LARS
doPelt # Run Pelt 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
getTprTnr Calculate the proportion of true positives and true negatives
jointSeg Joint segmentation of multivariate (copy number) signals
jointseg Joint segmentation of multivariate signals
modelSelection Model selection
plotSeg Plot signal and breakpoints with segment-level signal estimates
pruneByDP Exact segmentation of a multivariate signal using dynamic programming.
PSSeg Parent-Specific copy number segmentation
randomProfile Generate a random multi-dimensional profile with breakpoints and noise