classify_genome: classify the genome based on bed coordinates

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

classify the genome based on bed coordinates

Description

classify_genome Hierarchically classify the genome by coordinates in the list of bed files. Sequences in the first bed file are masked in the second and so on.

Usage

classify_genome(dnaSS, listOfBeds, verbose)

Arguments

dnaSS	DNAstringset object representing the genome assembly
listOfBeds	list of bed-like data.frames/data.tables with at least the columns chr, start and end.
verbose	logical, should updates be printed to the console?

Details

intersects, gaps and reduces overlapping intervals

Value

a list of granges matchin the listOfBeds

Examples

## Not run: 
# coming soon.

## End(Not run)

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.