inst/doc/PSSeg.R

In jointseg: Joint Segmentation of Multivariate (Copy Number) Signals

## ---- include=FALSE------------------------------------------------------
library("knitr")
opts_chunk$set(dev='png', fig.width=5, fig.height=5)

## ---- include=FALSE------------------------------------------------------
library("jointseg")

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data <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
str(data)

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table(data[["region"]])

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idxs <- sort(sample(1:nrow(data), 2e4))
plotSeg(data[idxs, ])

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K <- 10
bkp <- c(408,1632,3905, 5890,6709, 10481, 12647,14089,17345,18657)
len <- 2e4
sim <- getCopyNumberDataByResampling(len, bkp=bkp, minLength=500, regData=data)
datS <- sim$profile
str(datS)

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plotSeg(datS, sim$bkp)

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datS$c <- log2(datS$c)-1

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resRBS <- PSSeg(data=datS, K=2*K, method="RBS", stat=c("c", "d"), profile=TRUE)

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resRBS$prof[, "time"]

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plotSeg(datS, list(true=sim$bkp, est=resRBS$bestBkp))

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print(getTpFp(resRBS$bestBkp, sim$bkp, tol=5))

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perf <- sapply(0:10, FUN=function(tol) {
    getTpFp(resRBS$bestBkp, sim$bkp, tol=tol,relax = -1)
})
print(perf)

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sessionInfo()

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citation("jointseg")