findHotspots: Find breakpoint hotspots

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

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.

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.