Initialize a population, optionally guided by gene clusters

Creates the starting population. In "real" mode each gene value is drawn from an observed sample of that gene, so individuals preserve the marginal distribution of the data. In "binary" mode each gene is encoded as selected (1) or not selected (0).

Usage

initialize_population_cpp(
  genomic_data,
  population_size,
  seed = NULL,
  clusters = NULL,
  representation = "real"
)

Arguments

genomic_data

Numeric matrix of genomic data (rows: genes, columns: samples).

population_size

Number of individuals in the population.

seed

Optional random seed for reproducibility.

clusters

Optional vector of gene cluster assignments (length equal to the number of genes, non-negative integers).

representation

Either "real" (continuous expression values) or "binary" (gene selection indicators).

Value

Numeric matrix of initialized population (rows: individuals, columns: genes).

See also

evaluate_fitness_cpp(), selection_cpp(), crossover_cpp(), mutation_cpp(), replacement_cpp(), bioga_main_cpp()

Examples

genomic_data <- matrix(rnorm(100), nrow = 10, ncol = 10)
BioGA::initialize_population_cpp(genomic_data, population_size = 5, seed = 123)
#>             [,1]       [,2]     [,3]       [,4]        [,5]       [,6]
#> [1,]  0.06270301  1.6832769 1.463565 -0.1351125 -1.05541631 -0.2394497
#> [2,] -1.49079011 -0.4770160 2.558912 -0.1595557 -0.04804319 -1.9235357
#> [3,]  0.61886280 -0.4287279 2.558912  0.5639503 -1.71865548  0.5857998
#> [4,] -1.49079011 -0.3890261 2.558912 -1.6462332 -0.44972811  0.4242909
#> [5,]  0.24754278 -0.4770160 1.463565 -2.0166358 -0.04804319  0.3088376
#>            [,7]        [,8]       [,9]      [,10]
#> [1,] -0.4723847  0.71806477 -0.4393085 -0.6501188
#> [2,]  1.0104241  0.53409836 -0.1590448 -0.9046839
#> [3,] -0.4723847  1.49388563 -1.4871922  0.7206758
#> [4,] -0.6316866 -0.40966372 -0.1590448  0.2205800
#> [5,]  1.0104241 -0.05790095 -1.4871922  2.7254483