Sim_XGraSM_2013

Source: R/sim.R

Sim_XGraSM_2013

Sim_XGraSM_2013(
  dag,
  terms,
  IC_method = "IC_annotation",
  verbose = simona_opt$verbose
)

Methods

Sim_XGraSM_2013

The IC method is fixed to IC_annotation.

Being different from the "Relevance" and "SimIC_2010" methods that only use the IC of the MICA term, the XGraSM_2013 uses IC of all common ancestor terms of a and b. First it calculates the mean IC of all common ancestor terms with positive IC values:

IC_mean = mean_t(IC(t)) where t is an ancestor of both a and b, and IC(t) > 0

then similar to the Lin_1998 method, normalize to the average IC of a and b:

sim = IC_mean*2/(IC(a) + IC(b))

Paper link: doi:10.1186/1471-2105-14-284 .