Description Usage Arguments Value Author(s) See Also Examples
This function is a wrapper for convenient use of the PSCBS
segmentation method by PSSeg
. It applies the
segmentByPairedPSCBS
function and reshapes the results
1 |
Y |
A matrix of signals to be segmented, containing the following columns
|
... |
Arguments to be passed to
|
verbose |
A |
A list with a single element:
breakpoint positions
Morgane Pierre-Jean and Pierre Neuvial
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
## load known real copy number regions
affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
## generate a synthetic CN profile
K <- 10
len <- 1e4
sim <- getCopyNumberDataByResampling(len, K, minLength=100, regData=affyDat)
datS <- sim$profile
## run PSCBS segmentation
Y <- as.matrix(subset(datS, select=c(c, b, genotype)))
res <- doPSCBS(Y)
getTpFp(res$bkp, sim$bkp, tol=5, relax = -1) ## true and false positives
plotSeg(datS, breakpoints=list(sim$bkp, res$bkp))
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.