Calculate a peak cutoff

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Description

Calculates a peak cutoff value given an FDR, assuming a Poisson noise distribution estimated from the frequency of singleton and doubleton islands.

Usage

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peakCutoff(cov, fdr.cutoff = 0.001, k = 2:20)

Arguments

cov

The coverage object, e.g., an RleList object.

fdr.cutoff

The maximum-allowed FDR for calculating the cutoff.

k

The coverage levels at which to estimate an FDR value. The maximal value that is less than fdr.cutoff is chosen for calculating the cutoff. Usually best left to the default.

Value

A numeric value to use for calling peaks

Author(s)

D. Sarkar and M. Lawrence

See Also

islandDepthPlot for the graphical equivalent; the vignette for a bit more explanation.

Examples

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data(cstest)
cov <- coverage(resize(cstest$ctcf, width=200))
peakCutoff(cov)