Fpsn: Pruned dynamic programming algorithm
In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

Description Usage Arguments Details Value Author(s) References See Also Examples

Low-level API for the pruned dynamic programming algorithm (pDPA)

1	Fpsn(x, Kmax, mini = min(x), maxi = max(x))

`x`	A vector of double : the signal to be segmented
`Kmax`	Max number of segments
`mini`	Min value for the mean parameter of the segment
`maxi`	Max value for the mean parameter of the segment

This implementation uses functional pruning and segment neighborhood, and the L2-loss function

A list with a vector containing the position of the change-points

Guillem Rigaill

Rigaill, G. (2015). A pruned dynamic programming algorithm to recover the best segmentations with 1 to K_max change-points. Journal de la Societe Francaise de Statistique, 156(4), 180-205.

doDynamicProgramming for a higher-level function

## load known real copy number regions
affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)

## generate a synthetic CN profile
K <- 10
len <- 1e4
sim <- getCopyNumberDataByResampling(len, K, minLength=100, regData=affyDat)
datS <- sim$profile

## run pruned DPA segmentation
res <- Fpsn(datS[["c"]], Kmax=2*K+1)

## plot segmentation results for the true number of breakpoints
bkp <- res$t.est[K+1, 1:K]
plotSeg(datS, breakpoints=bkp)