doPSCBS {jointseg} | R Documentation |
Run Paired PSCBS segmentation
Description
This function is a wrapper for convenient use of the PSCBS
segmentation method by PSSeg
. It applies the
segmentByPairedPSCBS
function and reshapes the results
Usage
doPSCBS(Y, ..., verbose = FALSE)
Arguments
Y |
A matrix of signals to be segmented, containing the following columns
|
... |
Arguments to be passed to
|
verbose |
A |
Value
A list with a single element:
- bkp
breakpoint positions
Author(s)
Morgane Pierre-Jean and Pierre Neuvial
See Also
Examples
## 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)
[Package jointseg version 1.0.2 Index]