cnr: Simple creation of a CopyNumberRegions object

Description

Simple creation of a CopyNumberRegions object containing a single region.

Usage

cnr(start, stop=NULL, mean=1, chromosome=1, xScale=1e+06, ...)

Value

Return an CopyNumberRegions object.

Arguments

start, stop: Two numerics specifying the start and stop location of the region. If stop is NULL, then start[2] is used instead.
mean: A numeric specifying the mean level of the region.
chromosome: An integer specifying the chromosome ID.
xScale: The default scaling parameter used for start and stop, which is then also used for plotting genomic locations.
...: Additional arguments passed to CopyNumberRegions.

Author

Henrik Bengtsson

Examples

Run this code

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# Build up a tumor CN profile
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pT <- cnr(1,1000, 2) +
     cnr(400,500) +
     cnr(600,800) +
     cnr(600,700) +
     cnr(100,200) - cnr(850,900);
print(pT);


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulate CN signals from this profile
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cn <- simulateRawCopyNumbers(pT, n=2000, sd=1/2);
print(cn);


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Plot
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#aaaaaa", ylim=c(0,5));
drawLevels(pT, col="#ff0000", lwd=3);

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