library("aroma.cn")
if (Sys.getenv("_R_CHECK_FULL_") != "" && require("PSCBS")) {
# Load example ASCN data
data <- PSCBS::exampleData("paired.chr01")
R.oo::attachLocally(data)
# AD HOC: Robustification
CT[CT < 0] <- 0
CT[CT > 30] <- 30
# PSCBS segmentation
fit <- segmentByPairedPSCBS(CT, betaT=betaT, betaN=betaN, x=x, verbose=-10)
# Normalize
fitN <- normalizeBAFsByRegions(fit, verbose=-10)
devSet("tracks")
subplots(10, ncol=2, byrow=FALSE)
par(mar=c(1,3.5,1,0.5)+1)
plot(fit, subplots=TRUE)
plot(fitN, subplots=TRUE)
devSet("C1C2")
Clim <- c(0,4)
subplots(4, ncol=2, byrow=TRUE)
par(mar=c(1,3.5,1,0.5)+1)
plotC1C2(fit, Clim=Clim)
linesC1C2(fit)
title(main="(C1,C2)")
plotC1C2(fitN, Clim=Clim)
linesC1C2(fitN)
title(main="(C1,C2) - adjusted")
plotC1C2(fit, col="gray", Clim=Clim)
linesC1C2(fit, col="gray")
pointsC1C2(fitN)
linesC1C2(fitN)
title(main="(C1,C2) - both")
} # if (require("PSCBS"))
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