groupsim {Onassis}R Documentation

Method groupsim

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


[Package Onassis version 1.14.0 Index]