optimizer: Genetic algorithm for mRNA stability optimization

In santiago1234/iCodon: iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level

Genetic algorithm for mRNA stability optimization

Description

Genetic algorithm for mRNA stability optimization

Usage

optimizer(
  sequence_to_optimize,
  specie = "human",
  n_iterations = 15,
  make_more_optimal = T,
  mutation_Rate = 0.4,
  max_abs_val = Inf,
  n_Daughters = 3,
  random_seed = 123
)

Arguments

sequence_to_optimize	character, coding DNA sequence from start codon to stop codon
specie	character, species
n_iterations	integer, number of evolution iterations
make_more_optimal	logical, If true the sequence is optimized, if false
mutation_Rate	double, number of mutation to introduce at each iteration given as a probability (1 = max (mutate all positions), 0 = min (no mutations))
max_abs_val	A maximum value (absolute value) such that the sequences cannot go beyond that value. Infinite is used as default, in this case there is not a limit for the sequences
n_Daughters	integer, number of child sequences to explore at each iteration
random_seed	integer, random seed for getting reproducible results

Value

a [tibble][tibble::tibble-package], the best sequence at each iteration

Examples

suppressMessages(optimizer(test_seq, n_iterations = 1))

santiago1234/iCodon documentation built on Nov. 2, 2023, 2:03 p.m.