as.DNAcopy.CBS: Coerces a CBS object to a DNAcopy object

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Coerces a CBS object to a DNAcopy object

Description

Coerces a CBS object to a DNAcopy object.

Usage

## S3 method for class 'CBS'
as.DNAcopy(fit, ...)

Arguments

fit	A CBS object."
...	Not used.

Value

Returns a DNAcopy object (of the DNAcopy package).

Author(s)

Henrik Bengtsson

See Also

as.CBS(). For more information see CBS.

Examples

 
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
set.seed(0xBEEF)

# Number of loci
J <- 1000

mu <- double(J)
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)


 
# Coerce an CBS object to a DNAcopy object
fitD <- as.DNAcopy(fit)

# Coerce an DNAcopy object to a CBS object
fitC <- as.CBS(fitD)

# Sanity check
fitD2 <- as.DNAcopy(fit)
stopifnot(all.equal(fitD2, fitD))

fitC2 <- as.CBS(fitD2)
stopifnot(all.equal(fitC2, fitC))

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.