R Under development (unstable) (2024-02-16 r85931 ucrt) -- "Unsuffered Consequences"
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> # This test script calls a report generator which requires
> # the 'ggplot2' package, which in turn will require packages
> # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'.
> 
> # Only run this test in full testing mode
> if (Sys.getenv("_R_CHECK_FULL_") != "") {
+ library("PSCBS")
+ stext <- R.utils::stext
+ 
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # Load SNP microarray data
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ data <- PSCBS::exampleData("paired.chr01")
+ str(data)
+ 
+ data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT)
+ 
+ 
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # CBS segmentation
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # Drop single-locus outliers
+ dataS <- dropSegmentationOutliers(data)
+ 
+ # Speed up example by segmenting fewer loci
+ dataS <- dataS[seq(from=1, to=nrow(data), by=5),]
+ 
+ str(dataS)
+ 
+ gaps <- findLargeGaps(dataS, minLength=2e6)
+ knownSegments <- gapsToSegments(gaps)
+ 
+ # CBS segmentation
+ fit <- segmentByCBS(dataS, knownSegments=knownSegments,
+                             seed=0xBEEF, verbose=-10)
+ signalType(fit) <- "ratio"
+ plotTracks(fit)
+ 
+ 
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ # Call using the UCSF MAD caller (not recommended)
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ fitC <- callGainsAndLosses(fit)
+ plotTracks(fitC)
+ pars <- fitC$params$callGainsAndLosses
+ stext(side=3, pos=1/2, line=-1, substitute(sigma==x, list(x=sprintf("%.2f", pars$sigmaMAD))))
+ mu <- pars$muR
+ tau <- unlist(pars[c("tauLoss", "tauGain")], use.names=FALSE)
+ abline(h=mu, lty=2, lwd=2)
+ abline(h=tau, lwd=2)
+ mtext(side=4, at=tau[1], expression(Delta[LOSS]), adj=-0.2, cex=0.7, las=2, xpd=TRUE)
+ mtext(side=4, at=tau[2], expression(Delta[GAIN]), adj=-0.2, cex=0.7, las=2, xpd=TRUE)
+ title(main="CN caller: \"ucsf-mad\"")
+ 
+ 
+ # Caller to be implemented
+ deltaCN <- estimateDeltaCN(fit)
+ tau <- mu + 1/2*c(-1,+1)*deltaCN
+ abline(h=tau, lty=2, lwd=1, col="red")
+ 
+ 
+ 
+ } # if (Sys.getenv("_R_CHECK_FULL_"))
> 
> proc.time()
   user  system elapsed 
   0.15    0.00    0.15