Description Usage Arguments Details Value Author(s) References See Also Examples
Low-level API for the pruned dynamic programming algorithm (pDPA)
1 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## 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)
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