events: Events calling

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

Events calling

Description

Shortcut to call all simple and complex event types on JaBbA graph using standard settings on all event callers.

Usage

events(gg, verbose = TRUE, mark = FALSE, QRP = FALSE)

Arguments

gg	gGraph
verbose	verbose output Default: TRUE
mark	Default: FALSE
QRP	qrp events Default: FALSE

Value

gGraph with nodes and edges annotated with complex events in their node and edge metadata and in the graph meta data field $events

returns a gg with events found. A complete list of events include: amplifcation events (tyfonas, dm, cpxdm, bfb), chromothripsis, deletions, duplications, chromoplexies, tic's, and if QRP is True, qrp, qrpmix, qrppos, and qrpmin.

For more information on event calling please follow the tutorial in gGnome:

Classifying SV Events

See Also

simple, amp, chromothripsis, del, dup, chromoplexy, tic, qrp

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