hotspotter: Find hotspots of genomic events

In breakpointR: Find breakpoints in Strand-seq data

Description

Find hotspots of genomic events by using kernel density estimation.

Usage

hotspotter(gr.list, bw, pval = 1e-08)

Arguments

gr.list	A list or GRangesList-class with 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.

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

Examples

## Get example BreakPoint objects
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
exampleFiles <- list.files(exampleFolder, full.names=TRUE)
breakpoint.objects <- loadFromFiles(exampleFiles)
## Extract breakpoint coordinates
breaks <- lapply(breakpoint.objects, '[[', 'breaks')
## Get hotspot coordinates
hotspots <- hotspotter(gr.list=breaks, bw=1e6)

breakpointR documentation built on Nov. 8, 2020, 8:04 p.m.