hotspotter: Find hotspots of genomic events

In daewoooo/primatR: What the Package Does (TODO)

Find hotspots of genomic events

Description

Find hotspots of genomic events by using kernel density estimation.

Usage

hotspotter(gr, bw, pval = 1e-08, num.trial = 100)

Arguments

gr	A GRanges-class object containing the coordinates of the genomic events.
bw	Bandwidth used for kernel density estimation (see density).
pval	P-value cutoff for hotspots.
num.trial	A number of randomly subsampled set of genomic events.

Details

The hotspotter uses density to perform a KDE. A p-value is calculated by comparing the density profile of the genomic events with the density profile of a randomly subsampled set of genomic events. Due to this random sampling, the result can vary for each function call, most likely for hotspots whose p-value is close to the specified pval.

Value

A GRanges-class object containing coordinates of hotspots with p-values.

Author(s)

Aaron Taudt

daewoooo/primatR documentation built on Oct. 22, 2024, 9:41 p.m.