pickPeak: Identify peaks above a given threshold

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description

Given a vector of scores and a threshold, this function finds all peaks that exceed the threshold.

Usage

pickPeak(score, threshold, offset = 0, sub = FALSE)

Arguments

score	Numeric vector.
threshold	All values in score below this value are ignored.
offset	Offset to add to the determined peak locations.
sub	Logical. If this is FALSE (the default) for each region that exceeds the threshold only the global maximum is returned. Otherwise local maxima are returned as well.

Value

If sub = FALSE a numeric vector giving the location of all peaks. Otherwise a list with components

peaks	The same peak locations that are returned for sub = FALSE.
subPeaks	A list with one component for each entry in ‘peaks’ giving the location of local maxima.

Note

This function is used by callBindingSites for peak-calling.

Author(s)

Peter Humburg

See Also

callBindingSites, startScore, getCutoff

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.