pairsim {Onassis} | R Documentation

## `pairsim`

### Description

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

### Usage

    pairsim(object, term1, term2)

    ## S4 method for signature 'Similarity,character,character'
    pairsim(object, term1, term2)

### Arguments

`object` | instance of class `Similarity-class`
`term1` | The URI of the ontology term in the format http://purl.obolibrary.org/obo/Ontology_id (e.g 'http://purl.obolibrary.org/obo/CL_0000542')
`term2` | The URI of the ontology term

### Value

the semantic similarity of the two provided concepts

### Examples

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

[Package Onassis version 1.6.1 Index]