slide_genome: sliding window on a list of granges

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

sliding window on a list of granges

Description

slide_genome Hierarchically classify the genome by coordinates in the list of granges objects, returning the proportion of sequence each sliding window intersects

Usage

slide_genome(seqInfo, listOfGrs, windowSize, stepSize)

Arguments

seqInfo	seqinfo extracted from the genome assembly DNAstringset
listOfGrs	list of granges containing the regions to intersect
windowSize	numeric, giving the size in basepairs of the windows
stepSize	numeric, giving the step in basepairs between the windows

Details

intersects, gaps and reduces overlapping intervals within windows

Value

a data.table containing the amount of sequence covered in each window

Examples

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