Last data update: 2014.03.03
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R: Coerces a CBS object to a DNAcopy object
as.DNAcopy.CBS | R Documentation |
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."
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... |
Not used.
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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))
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(PSCBS)
PSCBS v0.61.0 (2016-02-03) successfully loaded. See ?PSCBS for help.
Attaching package: 'PSCBS'
The following objects are masked from 'package:base':
append, load
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PSCBS/as.DNAcopy.CBS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: as.DNAcopy.CBS
> ### Title: Coerces a CBS object to a DNAcopy object
> ### Aliases: as.DNAcopy.CBS CBS.as.DNAcopy as.DNAcopy,CBS-method
> ### Keywords: internal methods
>
> ### ** 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)
sampleName chromosome start end nbrOfLoci mean
1 <NA> 0 55167.82 20774251 201 0.0164
2 <NA> 0 20774250.85 29320105 99 1.0474
3 <NA> 0 29320104.86 65874675 298 -0.0203
4 <NA> 0 65874675.06 81348129 151 -1.0813
5 <NA> 0 81348129.20 99910827 200 -0.0612
> 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))
list()
>
>
>
>
>
>
> dev.off()
null device
1
>
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