reciprocal: Get reciprical connected junctions

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

Get reciprical connected junctions

Description

Identifies reciprocally connected junctions, i.e. breakends from non-identical junctions that are "linked" by an inter-breakpoint distance less than a given threshold. Edges and nodes are marked by the "ecluster" metadata field

Usage

reciprocal(gg, thresh = 5e+05, max.small = 10000)

Arguments

gg	gGraph
thresh	threshold for edge clusters. Default: 5e5
max.small	max small threshold for edge clusters. Default: 1e4

Details

Reciprocal junctions are junctions with breakends that are mutually adjacent and opposite.

i.e. breakends from non-identical junctions that are "linked" by an inter-breakpoint distance less than a given threshold. Edges and nodes are marked by the "ecluster" metadata field

Value

gGraph with $ecluster marking on nodes and edges labeling unique reciprocal events

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.