Description Usage Arguments Details Value Author(s) Examples
Prune the CBS profile by dropping change points that are too small, where "too small" means that the amplitude of the change points is less than a multiple of the overall standard deviation of the copy-number signals.
1 2 | ## S3 method for class 'CBS'
pruneBySdUndo(fit, rho=3, sigma="DNAcopy", ..., verbose=FALSE)
|
fit |
A |
rho |
A positive |
sigma |
The whole-genome standard deviation of the locus-level copy number signals. The default is to calculate it from the data and as done in the DNAcopy package. |
... |
(Optional) Additional arguments passed to the standard deviation estimator function. |
verbose |
See |
This method corresponds to using the undo
argument when calling
segmentByCBS
(), which in turn corresponds to using the
undo.splits="sdundo"
and undo.SD
of the underlying
segment
method.
Returns a CBS
object (of the same class as fit
).
Henrik Bengtsson, 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 24 25 26 27 28 29 30 31 32 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
set.seed(0xBEEF)
# Number of loci
J <- 1000
mu <- double(J)
mu[1:100] <- mu[1:100] + 0.3
mu[200:300] <- mu[200:300] + 1
mu[350:400] <- NA # centromere
mu[650:800] <- mu[650:800] - 1
eps <- rnorm(J, sd=1/2)
y <- mu + eps
x <- sort(runif(length(y), max=length(y))) * 1e5
w <- runif(J)
w[650:800] <- 0.001
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Segmentation
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fit <- segmentByCBS(y, x=x)
print(fit)
plotTracks(fit)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Post-segmentation pruning
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fitP <- pruneBySdUndo(fit, rho=1)
drawLevels(fitP, col="red")
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