GroupSim_pairwise_avg

GroupSim_pairwise_avg

GroupSim_pairwise_avg(
  dag,
  group1,
  group2,
  term_sim_method = NULL,
  IC_method = NULL,
  verbose = simona_opt$verbose,
  ...
)

Methods

GroupSim_pairwise_avg

Denote S(a, b) as the semantic similarity between terms a and b where a is from group1 and b is from group2, The similarity between group1 and group2 is the average similarity of every pair of individual terms in the two groups:

group_sim = mean_{a in group1, b in group2}(S(a, b))

The term semantic similarity method and the IC method can be set via control argument:

group_sim(dag, group1, group2, method = "GroupSim_pairwise_avg"
    control = list(term_sim_method = "Sim_Lin_1998", IC_method = "IC_annotation")`.

Other parameters for the term_sim_method can also be set in the control list.

Pape link: doi:10.1093/bioinformatics/btg153 .