simulate_pan: simulate_pan

In gtonkinhill/panstripe: Pangenome Plots

simulate_pan

Description

Simulates a pangenome presence/absence matrix and accompanying core phylogeny

Usage

simulate_pan(
  ngenomes = 50,
  rate = 1e-05,
  genome_length = 2000,
  fn_error_rate = 1,
  fp_error_rate = 3,
  mean_trans_size = 3,
  Q = 1,
  bf = c(0.3, 0.2)
)

Arguments

ngenomes	number of genomes to simulate
rate	rate of gene gain/loss events
genome_length	number of genes
fn_error_rate	false negative error rate
fp_error_rate	false positive error rate
mean_trans_size	mean size of the number of genes gained or lost per event
Q	the rate matrix (default=1)
bf	the base frequencies (default=c(0.3,0.2))

Value

A list comprising of a binary gene presence/absence matrix and a core phylogeny

Examples

pan <- simulate_pan()

gtonkinhill/panstripe documentation built on Feb. 27, 2025, 9:01 p.m.