simulate_recombination: Simulates the evolution of a family of sequences by taking...

In sams25/rcombinator_old: Tools to Simulate the Evolution of Genetic Sequences

Description

Simulates the evolution of a family of sequences by taking into consideration both point mutation and burst events

Usage

simulate_recombination(sequences, num_jumps,
  transition_matrix = get_k80_matrix(10^6), burst_threshold = 0.2,
  burst_mean = 1, flip_probability = 0.3, max_copy_number = 30,
  dist_method = "levenshtein", num_dist_matrices = 0, options = NULL,
  save_sequences = FALSE, save_file = NULL)

Arguments

sequences	The original sequences to begin with
num_jumps	The number of time steps to simulate for
transition_matrix	The transition matrix for the point mutations
burst_mean	The mean (for a Poisson distribution) increase in copy number during a burst event
burst_threshhold	The probability of a burst even occurring

Value

A list of sequences that have evolved over time with both point mutation and recombination

sams25/rcombinator_old documentation built on May 28, 2019, 8:40 a.m.