Calculate the information content for each ontology term

this function will calculate the information content of each provided term based on a list of ancestors, which is a named list of terms with ancestor identifiers as their values. Can be calculated using get_ontology_ancestry(). The information content is calculated as -log2(number descendant/total terms in the ontology). More information can be found here.

Usage

calculate_information_content(ancestor_list)

Arguments

ancestor_list

List. Named list of terms with ancestor identifiers as their values

Value

A named list of each term and their information content as values.

Examples

# information content from the descendant counts of a toy ontology
onto <- data.table::data.table(
  parent = c("a", "b", "b", "b", "c"),
  child = c("b", "c", "d", "e", "f")
)
ancestry <- get_ontology_ancestry(onto)
unlist(calculate_information_content(ancestry$descendants))
#>         a         b         c         d         e         f 
#> 0.0000000 0.1823216 1.0986123 1.7917595 1.7917595 1.7917595