Calculate the Wang similarities between terms

This function calculates the Wang similarity for a set of temrs, based on the DAG for a given ontology.

Usage

calculate_wang_sim(terms, parent_child_dt, weights, add_self = FALSE)

Arguments

terms

String vector. The terms for which to calculate the Wang similarity.

parent_child_dt

data.table. The data.table with column parent and child. You also need to have a type column for the Wang similarity to provide the weights for the relationships.

weights

Named numeric. The relationship of type to weight for this specific edge. For example c("part_of" = 0.8, "is_a" = 0.6).

add_self

Boolean. Shall self-similarities be added. Defaults to FALSE.

Value

A data.table with the calculated similarities.

Examples

# Wang similarity for a subset of terms only
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)
calculate_wang_sim(c("c", "d", "f"), onto, weights = weights)
#>     term1  term2      sims
#>    <char> <char>     <num>
#> 1:      c      d 0.5901639
#> 2:      c      f 0.7960848
#> 3:      d      f 0.4698206