findHotspots: Find breakpoint hotspots
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value

Find breakpoint hotspots with kernel density estimation (KDE).

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

`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`.

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.

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

AneuFinder documentation built on Nov. 8, 2020, 7:44 p.m.