peakCutoff: Calculate a peak cutoff

In Bioconductor/chipseq: chipseq: A package for analyzing chipseq data

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)

Bioconductor/chipseq documentation built on Nov. 2, 2024, 7:23 a.m.