R Under development (unstable) (2024-02-16 r85931 ucrt) -- "Unsuffered Consequences"
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> library("PSCBS")
PSCBS v0.67.0 successfully loaded. See ?PSCBS for help.
> 
> # Simulating copy-number data
> set.seed(0xBEEF)
> 
> # Simulate CN data
> J <- 1000
> mu <- double(J)
> mu[200:300] <- mu[200:300] + 1
> mu[350:400] <- NA # centromere
> mu[650:800] <- mu[650:800] - 1
> eps <- rnorm(J, sd=1/2)
> y <- mu + eps
> x <- seq(from=1, to=100e6, length.out=J)
> 
> data <- data.frame(chromosome=0L, x=x)
> 
> gaps <- findLargeGaps(x=x, minLength=1e6)
> print(gaps)
[1] start  end    length
<0 rows> (or 0-length row.names)
> stopifnot(is.data.frame(gaps))
> stopifnot(nrow(gaps) == 0L)
> segs <- gapsToSegments(gaps)
> print(segs)
  chromosome start end
1          0  -Inf Inf
> stopifnot(is.data.frame(segs))
> stopifnot(nrow(segs) == 1L)
> 
> 
> gaps <- findLargeGaps(data, minLength=1e6)
> print(gaps)
[1] chromosome start      end       
<0 rows> (or 0-length row.names)
> stopifnot(is.data.frame(gaps))
> stopifnot(nrow(gaps) == 0L)
> segs <- gapsToSegments(gaps)
> print(segs)
  chromosome start end
1          0  -Inf Inf
> stopifnot(is.data.frame(segs))
> stopifnot(nrow(segs) == 1L)
> 
> 
> ## Add missing values
> data2 <- data
> data$x[30e6 < x & x < 50e6] <- NA
> gaps <- findLargeGaps(data, minLength=1e6)
> print(gaps)
  chromosome    start      end   length
1          0 29929932 50050050 20120118
> stopifnot(is.data.frame(gaps))
> stopifnot(nrow(gaps) == 1L)
> segs <- gapsToSegments(gaps)
> print(segs)
  chromosome    start      end   length
1          0     -Inf 29929931      Inf
2          0 29929932 50050050 20120118
3          0 50050051      Inf      Inf
> stopifnot(is.data.frame(segs))
> stopifnot(nrow(segs) == 3L)
> 
> 
> 
> # BUG FIX: Issue #6
> gaps <- findLargeGaps(chromosome=rep(1,10), x=1:10, minLength=2)
> print(gaps)
[1] chromosome start      end       
<0 rows> (or 0-length row.names)
> stopifnot(is.data.frame(gaps))
> stopifnot(nrow(gaps) == 0L)
> # BUG FIX: Issue #9
> segs <- gapsToSegments(gaps)
> print(segs)
  chromosome start end
1          0  -Inf Inf
> stopifnot(is.data.frame(segs))
> stopifnot(nrow(segs) == 1L)
> 
> 
> # BUG FIX: PSCBS GitHub Issue #8
> gaps <- try({
+   findLargeGaps(chromosome=rep(1,3), x=as.numeric(1:3), minLength=1)
+ })
Error in findLargeGaps.default(chromosome = rep(1, 3), x = as.numeric(1:3),  : 
  Cannot identify large gaps. Argument 'resolution' (=1) is not strictly smaller than 'minLength' (=1).
> stopifnot(inherits(gaps, "try-error"))
> 
> proc.time()
   user  system elapsed 
   0.34    0.09    0.56