peakCutoff {chipseq} | R Documentation

## Calculate a peak cutoff

### Description

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

### Usage

    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

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

[Package chipseq version 1.36.0 Index]