groupsim: Method groupsim

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method computes the semantic similarity between two groups of terms of a given ontology.

Usage

groupsim(object, termList1, termList2)

## S4 method for signature 'Similarity,character,character'
groupsim(object, termList1,
  termList2)

Arguments

object	instance of class Similarity-class
termList1	A vector of URIs of ontology terms in the format http://purl.obolibrary.org/obo/Ontology_id (e.g http://purl.obolibrary.org/obo/BTO_0004732)
termList2	A vector of URIs of ontology terms

Value

the semantic similarity of the two provided groups of concepts

Examples

sim <- new('Similarity')
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
ontology(sim) <- obo
pairwiseConfig(sim) <- listSimilarities()$pairwiseMeasures[9]
groupConfig(sim) <- listSimilarities()$groupwiseMeasures[3]
similarity <- groupsim(sim, c('http://purl.obolibrary.org/obo/CL_0000542',
 'http://purl.obolibrary.org/obo/CL_0000236'),
c('http://purl.obolibrary.org/obo/CL_0000000'))
similarity

Onassis documentation built on Nov. 8, 2020, 8:18 p.m.