This vignette describes how to use the jointseg
package to partition bivariate DNA copy number signals from SNP array data into segments of constant parent-specific copy number. We demonstrate the use of the PSSeg
function of this package for applying two different strategies. Both strategies consist in first identifying a list of candidate change points through a fast (greedy) segmentation method, and then to prune this list is using dynamic programming [1]. The segmentation method presented here is Recursive Binary Segmentation (RBS, [2]). We refer to [3] for a more comprehensive performance assessment of this method and other segmentation methods.
\paragraph{keywords:} segmentation, change point model, binary segmentation, dynamic programming, DNA copy number, parent-specific copy number.
Please see Appendix \ref{citation} for citing jointseg
.
library("jointseg")
HERE
library("knitr") opts_chunk$set(dev='png', fig.width=5, fig.height=5) opts_knit$set(eval.after = "fig.cap")
This vignette illustrates how the jointseg
package may be used to generate a variety of copy-number profiles from the same biological ``truth''. Such profiles have been used to compare the performance of segmentation methods in [3].
jointseg
citation("jointseg")
library("jointseg")
The parameters are defined as follows:
n <- 1e4 ## signal length bkp <- c(2334, 6121) ## breakpoint positions regions <- c("(1,1)", "(1,2)", "(0,2)") ## copy number regions
ylims <- cbind(c(0, 5), c(-0.1, 1.1)) colG <- rep("#88888855", n) hetCol <- "#00000088"
For convenience we define a custom plot function for this vignette:
plotFUN <- function(dataSet, tumorFraction) { regDat <- acnr::loadCnRegionData(dataSet=dataSet, tumorFraction=tumorFraction) sim <- getCopyNumberDataByResampling(n, bkp=bkp, regions=regions, regData=regDat) dat <- sim$profile wHet <- which(dat$genotype==1/2) colGG <- colG colGG[wHet] <- hetCol plotSeg(dat, sim$bkp, col=colGG) }
ds <- "GSE29172"
pct <- 1 plotFUN(ds, pct)
plotFUN(ds, pct)
pct <- 0.7 plotFUN(ds, pct)
pct <- 0.5 plotFUN(ds, pct)
ds <- "GSE11976"
sessionInfo()
[1] Bellman, Richard. 1961. "On the Approximation of Curves by Line Segments Using Dynamic Programming." Communications of the ACM 4 (6). ACM: 284.
[2] Gey, Servane, et al. 2008. "Using CART to Detect Multiple Change Points in the Mean for Large Sample." https://hal.archives-ouvertes.fr/hal-00327146.
[3] Pierre-Jean, Morgane, et al. 2015. "Performance Evaluation of DNA Copy Number Segmentation Methods." Briefings in Bioinformatics, no. 4: 600-615.
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