Description Usage Arguments Value Author(s) Examples
Calculate the number of true positives and false positives among candidate breakpoints
1 | getTpFp(candidates, trueBkp, tol, relax = -1)
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candidates |
Breakpoints found by the methods |
trueBkp |
True breakpoints |
tol |
Tolerance on the position of candidate breakpoints called true |
relax |
Controls the way multiple breapoints within tolerance area are recorded.
|
A list with elements:
The number of true positives
The number of false positives
Morgane Pierre-Jean and Pierre Neuvial
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## load known real copy number regions
affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=0.7)
## generate a synthetic CN profile
K <- 10
len <- 2e4
sim <- getCopyNumberDataByResampling(len, K, minLength=100, regData=affyDat)
datS <- sim$profile
## (group-)fused Lasso segmentation
res <- PSSeg(data=datS, K=2*K, method="GFLars", stat="c", profile=TRUE)
## results of the initial (group-)fused lasso segmentation
getTpFp(res$initBkp, sim$bkp, tol=10, relax=-1)
getTpFp(res$initBkp, sim$bkp, tol=10, relax=0)
getTpFp(res$initBkp, sim$bkp, tol=10, relax=1)
plotSeg(datS, breakpoints=list(sim$bkp, res$initBkp))
## results after pruning (group-)fused Lasso candidates by dynamic programming)
getTpFp(res$bestBkp, sim$bkp, tol=10, relax=-1)
getTpFp(res$bestBkp, sim$bkp, tol=10, relax=0)
getTpFp(res$bestBkp, sim$bkp, tol=10, relax=1)
plotSeg(datS, breakpoints=list(sim$bkp, res$bestBkp))
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