R Under development (unstable) (2025-04-17 r88153 ucrt) -- "Unsuffered Consequences"
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> set.seed(0xBEEF)
> 
> # Number of loci
> J <- 1000
> 
> mu <- double(J)
> mu[200:300] <- mu[200:300] + 1
> mu[350:400] <- NA_real_ # centromere
> mu[650:800] <- mu[650:800] - 1
> eps <- rnorm(J, sd=1/2)
> y <- mu + eps
> x <- sort(runif(length(y), max=length(y))) * 1e5
> 
> knownSegments <- data.frame(
+   chromosome=c(    0,   0),
+   start     =x[c(  1, 401)],
+   end       =x[c(349,   J)]
+ )
> 
> fit2 <- PSCBS::segmentByCBS(y, x=x, knownSegments=knownSegments)
> 
> proc.time()
   user  system elapsed 
   0.57    0.10    0.68