R Under development (unstable) (2024-02-16 r85931 ucrt) -- "Unsuffered Consequences"
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> library("aroma.cn")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, load, save

R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings

Loading required package: aroma.core
Loading required package: R.filesets
R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help.

Attaching package: 'R.filesets'

The following object is masked from 'package:R.utils':

    validate

The following objects are masked from 'package:base':

    append, readLines

Loading required package: R.devices
R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
aroma.core v3.3.0 (2022-11-15 18:30:13 UTC) successfully loaded. See ?aroma.core for help.

Attaching package: 'aroma.core'

The following objects are masked from 'package:base':

    .Machine, colMeans, colSums, library, require, write

Loading required package: aroma.light
aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help.

Attaching package: 'aroma.light'

The following objects are masked from 'package:aroma.core':

    callNaiveGenotypes, normalizeTumorBoost

aroma.cn v1.7.1 successfully loaded. See ?aroma.cn for help.
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Build up a tumor CN profile
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> pT <- cnr(1,1000, 2) +
+      cnr(400,500) +
+      cnr(600,800) +
+      cnr(600,700) +
+      cnr(100,200) - cnr(850,900)
> print(pT)
CopyNumberRegions:
Number of regions: 10
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Simulate CN signals from this profile
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cn <- simulateRawCopyNumbers(pT, n=2000, sd=1/2)
> print(cn)
RawCopyNumbers:
Name: <none>
Number of rows: 2000
Number of columns: 3
Columns: chromosome [numeric], x [numeric], cn [numeric]
Chromosomes: 1 [1]
Number of loci: 2000
Position range: [1e+06,1e+09]
Mean distance between loci: 499750
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Plot
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> plot(cn, col="#aaaaaa", ylim=c(0,5))
> drawLevels(pT, col="#ff0000", lwd=3)
> 
> proc.time()
   user  system elapsed 
   0.68    0.14    0.81