hotspotter: Find hotspots of genomic events
In daewoooo/YeastSCElocatoR: Find SCEs in haploid Strand-seq data

Description Usage Arguments Details Value Author(s) Examples

Find hotspots of genomic events by using kernel density estimation.

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

`gr.list`	A list with `GRanges` object containing the coordinates of the genomic events.
`bw`	Bandwidth used for kernel density estimation (see `density`).
`pval`	P-value cutoff for hotspots.

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.

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

Aaron Taudt

## Get example BreakPoint objects
data(example_BreakPoints)
## Extract breakpoint coordinates
breaks <- lapply(example_BreakPoints, '[[', 'breaks')
## Get hotspot coordinates
hotspots <- hotspotter(breaks, bw=1e6)