Calculates the critical value

This function calculates the critical value for a given ontology similarity matrix.

Usage

calculate_critical_value(x, alpha, permutations = 100000L, seed = 10101L)

Arguments

x

Numerical matrix or OntologySim class, see OntologySim(). This function tends to be slower on matrices compared to the OntologySim class.

alpha

Float. The alpha value. For example, 0.001 would mean that the critical value is smaller than 0.1 percentile of the random permutations.

permutations

Number of random permutations.

seed

Integer. For reproducibility purposes

Value

The critical value.

Examples

# critical value of a Wang similarity matrix at alpha 0.1
onto <- data.table::data.table(
  parent = c("a", "b", "b", "b", "c"),
  child = c("b", "c", "d", "e", "f"),
  type = c("part_of", "part_of", "part_of", "is_a", "is_a")
)
weights <- c(part_of = 0.8, is_a = 0.6)
sim_mat <- calculate_wang_sim_mat(onto, weights = weights)
calculate_critical_value(sim_mat, alpha = 0.1)
#> [1] 0.7641509