aroma.core (version 2.14.0)

segmentByMPCBS.RawGenomicSignals: Segment copy numbers using the multi-platform CBS (mpCBS) method

Description

Segment copy numbers using the multi-platform CBS (mpCBS) method of the mpcbs package.

Usage

## S3 method for class 'RawGenomicSignals':
segmentByMPCBS(this, ..., cache=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to the segmentation function.

verbose

See Verbose.

Value

• Returns the fit object.

Details

Internally mpcbs.mbic() of the mpcbs package is used for segmenting the signals. This segmentation method does not support weighted segmentation.

See Also

For more information see RawGenomicSignals.

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data from multiple platforms
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Piecewise-constant copy-number state function
cnState <- function(x, ...) {
  n <- length(x)
  mu <- double(n)
  mu[20e6 <= x & x <= 30e6] <- +1
  mu[65e6 <= x & x <= 80e6] <- -1
  mu
} # cnState()

xMax <- 100e6

Js <- c(200, 400, 100)
bs <- c(1, 1.4, 0.5)
as <- c(0, +0.5, -0.5)
sds <- c(0.5, 0.3, 0.8)

cnList <- list()
for (kk in seq(along=Js)) {
  J <- Js[kk]
  a <- as[kk]
  b <- bs[kk]
  sd <- sds[kk]
  x <- sort(runif(J, max=xMax))
  mu <- a + b * cnState(x)
  eps <- rnorm(J, sd=sd)
  y <- mu + eps
  cn <- RawCopyNumbers(y, x)
  cnList[[kk]] <- cn
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Merge platform data (record their sources in 'id')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cn <- Reduce(append, cnList)
plot(cn, ylim=c(-3,3), col=cn$id)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Segment
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
legend <- c()

if (require("DNAcopy")) {
  fit <- segmentByCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="white", lwd=6)
  drawLevels(cnr, col="red", lwd=3)
  legend <- c(legend, red="CBS")
}


if (require("mpcbs")) {
  fit <- segmentByMPCBS(cn)
  cnr <- extractCopyNumberRegions(fit)
  print(cnr)
  drawLevels(cnr, col="white", lwd=6)
  drawLevels(cnr, col="blue", lwd=3)
  legend <- c(legend, blue="MPCBS")
}


if (length(legend) > 0) {
  legend("topleft", pch=19, col=names(legend), legend, bty="n", horiz=TRUE)
}