Running examples in ‘aroma.core-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: segmentByCBS.RawGenomicSignals
> ### Title: Segment copy numbers using the CBS method
> ### Aliases: segmentByCBS.RawGenomicSignals RawGenomicSignals.segmentByCBS
> ###   segmentByCBS,RawGenomicSignals-method
> ### Keywords: internal methods IO
> 
> ### ** Examples
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Simulating copy-number data
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Number of loci
> J <- 500
> 
> mu <- double(J)
> mu[100:150] <- mu[100:150] + 1
> mu[320:400] <- mu[320:400] - 1
> eps <- rnorm(J, sd=1/2)
> y <- mu + eps
> x <- sort(runif(length(y), max=length(y))) * 1e5
> w <- runif(J)
> w[320:400] <- 0.001
> 
> 
> cn <- RawCopyNumbers(y, x)
> print(cn)
RawCopyNumbers:
Name: <none>
Number of rows: 500
Number of columns: 3
Columns: chromosome [numeric], x [numeric], cn [numeric]
Chromosomes: 0 [1]
Number of loci: 500
Position range: [82113.1,4.98136e+07]
Mean distance between loci: 99662.3
> 
> plot(cn, ylim=c(-3,3), col="#aaaaaa", xlab="Position (Mb)")
> 
> cnS <- binnedSmoothing(cn, by=500e3)
> print(cnS)
RawCopyNumbers:
Name: <none>
Number of rows: 100
Number of columns: 3
Columns: chromosome [numeric], x [numeric], cn [numeric]
Chromosomes:  [0]
Number of loci: 100
> lines(cnS, col="black", lwd=3)
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Segment
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> legend <- c()
> 
> if (require("DNAcopy")) {
+   fit <- segmentByCBS(cn)
+   cnr <- extractCopyNumberRegions(fit)
+   print(cnr)
+   drawLevels(cnr, col="red", lwd=3)
+   legend <- c(legend, red="CBS")
+ }
Loading required package: DNAcopy
CopyNumberRegions:
Number of regions: 5
> 
> if (require("GLAD") && packageVersion("GLAD") != "9.9.9") {
+   fit <- segmentByGLAD(cn)
+   cnr <- extractCopyNumberRegions(fit)
+   print(cnr)
+   drawLevels(cnr, col="blue", lwd=3)
+   legend <- c(legend, blue="GLAD")
+ }
Loading required package: GLAD

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.

Error in UseMethod("as.profileCGH") : 
  no applicable method for 'as.profileCGH' applied to an object of class "data.frame"
Calls: segmentByGLAD -> segmentByGLAD.RawGenomicSignals -> <Anonymous>
Execution halted