simple: Simple Event Calling

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

Simple Event Calling

Description

Call simple events in gGraph

Usage

simple(
  gg,
  reciprocal.thresh = 10000,
  tra.pad = 1e+06,
  mark = TRUE,
  mark.col = "purple"
)

Arguments

gg	gGraph, must have 'cn' node and edge annotation
reciprocal.thresh	reciprocal threshold added to alt.shadows to find translocations Default: 1e4
tra.pad	translocation padding to add on when finding locations Default: 1e6
mark	logical flag specifying whether to mark fold backs Default: TRUE
mark.col	character specifying colors to mark graph with Default: 'purple'

Details

simple event calling includes 3 events: inversion, inverted duplication, and translocation.

For how to run this function: Simple

Value

gGraph object containing labeling the putative event

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