segmentByCBS.RawGenomicSignals {aroma.core} | R Documentation |
Segment copy numbers using the CBS method of the DNAcopy package.
## S3 method for class 'RawGenomicSignals': segmentByCBS(this, ..., cache=FALSE, force=FALSE, verbose=FALSE)
... |
Additional arguments passed to the segmentation function. |
verbose |
See Verbose . |
Internally segment
is used to segment the signals.
This segmentation method support weighted segmentation.
Returns the fit object.
Henrik Bengtsson (http://www.braju.com/R/)
For more information see RawGenomicSignals
.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Simulating copy-number data # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Number of loci J <- 1000 mu <- double(J) mu[200:300] <- mu[200:300] + 1 mu[650:800] <- mu[650:800] - 1 eps <- rnorm(J, sd=1/2) y <- mu + eps x <- sort(runif(length(y), max=length(y))) w <- runif(J) w[650:800] <- 0.001 cn <- RawCopyNumbers(y, x) print(cn) plot(cn, col="#aaaaaa") cnS <- binnedSmoothing(cn, by=10) print(cnS) 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") } if (require("GLAD")) { fit <- segmentByGLAD(cn) cnr <- extractCopyNumberRegions(fit) print(cnr) drawLevels(cnr, col="blue", lwd=3) legend <- c(legend, blue="GLAD") } if (require("HaarSeg")) { fit <- segmentByHaarSeg(cn) cnr <- extractCopyNumberRegions(fit) print(cnr) drawLevels(cnr, col="orange", lwd=3) legend <- c(legend, orange="HaarSeg") } legend("topleft", pch=19, col=names(legend), legend, bty="n", horiz=TRUE)