hotspotter.variable {AneuFinder} | R Documentation

## Find hotspots of genomic events

### Description

Find hotspots of genomic events by using kernel density estimation.

### Usage

    hotspotter.variable(breakpoints, confint, pval = 0.05, spacing.bp = 5000)

### Arguments

`breakpoints` | A list with `GRanges-class` object containing the coordinates of the genomic events and their confidence intervals.
`confint` | Confidence interval that was used for breakpoint estimation.
`pval` | P-value cutoff for hotspots.
`spacing.bp` | Spacing of datapoints for KDE in basepairs.

### Details

The hotspotter uses a gaussian kernel with variable bandwidth to perform a KDE. The bandwidth depends on the confidence intervals of the breakpoints. 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 (bootstrapping).

### Value

A list of `GRanges-class` objects containing 1) coordinates of hotspots and 2) p-values within the hotspot.

### Author(s)

Aaron Taudt

[Package AneuFinder version 1.12.1 Index]