findHotspots {AneuFinder} | R Documentation

## Find breakpoint hotspots

### Description

Find breakpoint hotspots with kernel density estimation (KDE).

### Usage

    findHotspots(models, bw, pval = 0.05, spacing.bp = 5000, filename = NULL)

### Arguments

`models` | A list of `GRanges-class` or `aneuHMM` objects or a character vector with files that contain such objects.
`bw` | Bandwidth used for kernel density estimation (see `density`).
`pval` | P-value cutoff for hotspots.
`spacing.bp` | Spacing of datapoints for KDE in basepairs.
`filename` | Will write hotspot coordinates and densities to the specified file. Endings "_breakpoint-hotspots.bed.gz" and "_breakpoint-densities.wig.gz" will be appended to `filename`.

### Details

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

[Package AneuFinder version 1.12.1 Index]