segmentByRBS: Recursive Binary Segmentation (low-level)

In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

Description

Low-level function for multivariate Recursive Binary Segmentation (RBS)

Usage

segmentByRBS(Y, K, minRegionSize = 2, verbose = FALSE)

Arguments

Y	A n*p signal to be segmented
K	The number of change points to find
minRegionSize	Regions with less than minRegionSize are not split
verbose	A logical value: should extra information be output ? Defaults to FALSE.

Details

This function recrusively looks for the best candidate change point according to binary segmentation. This is the low-level function. It is generally advised to use the wrapper doRBS which also works on data frames and has a convenient argument stat.

See jointSeg for combining recursive binary segmentation with pruning by dynamic programming (pruneByDP).

See PSSeg for segmenting genomic signals from SNP arrays.

Each dimension of the original signal is scaled before segmentation, using estimateSd.

Value

A list with elements:

bkp	A vector of K estimated breakpoint positions, sorted by order of appearance
rse	the residual squared error (RSE) for the successive segmentations
gain	The gain provided by each breakpoints in terms of difference between RSE

Author(s)

Morgane Pierre-Jean and Pierre Neuvial

References

Gey, S., & Lebarbier, E. (2008). Using CART to Detect Multiple Change Points in the Mean for Large Sample. http://hal.archives-ouvertes.fr/hal-00327146/

See Also

PSSeg, jointSeg, doRBS, pruneByDP

Examples

p <- 2
trueK <- 10
len <- 1e4
sim <- randomProfile(len, trueK, 1, p)
Y <- sim$profile
K <- 2*trueK
res <- segmentByRBS(Y, K)
getTpFp(res$bkp, sim$bkp, tol=10, relax = -1)   ## true and false positives

cols <- rep(2, K)
cols[1:trueK] <- 3
par(mfrow=c(p,1))
for (ii in 1:p) {
    plot(Y[, ii], pch=19, cex=0.2)
    abline(v=res$bkp[1:trueK], col= cols)
    abline(v=sim$bkp, col=8, lty=2)
}

## NA:s in one dimension at a true breakpoint
jj <- sim$bkp[1]
Y[jj-seq(-10, 10), p] <- NA
res2 <- segmentByRBS(Y, K)
getTpFp(res2$bkp, sim$bkp, tol=10, relax = -1)   ## true and false positives

## NA:s in both dimensions at a true breakpoint
Y[jj-seq(-10, 10), ] <- NA
res3 <- segmentByRBS(Y, K)
getTpFp(res3$bkp, sim$bkp, tol=10, relax = -1)   ## true and false positives

mpierrejean/jointSeg documentation built on May 23, 2019, 6:28 a.m.