findHotspots: Find breakpoint hotspots

Description Usage Arguments Details Value

View source: R/hotspotter.R

Description

Find breakpoint hotspots with kernel density estimation (KDE).

Usage

1
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.


AneuFinder documentation built on Nov. 18, 2018, 6 p.m.