sim: 'sim'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method computes the similarities of the entities annotated in a object fo class Onassis-class.

Usage

sim(onassis = NA, ...)

## S4 method for signature 'Onassis'
sim(onassis, iconf = "sanchez", pairconf = "lin",
  groupconf = "bma")

Arguments

onassis	instance of class Onassis-class
...	Optional parameters
iconf	the information content measure see pairwiseConfig help for details
pairconf	the pairwse measure to compute semantic similarity between single concepts. See pariwiseConfig help for details
groupconf	the groupwise measure to compute semantic similarity between groups of concepts. See groupConfig help for details

Value

an instance of Onassis-class with computed similarities

Examples

geo_chip <- readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds', package='Onassis'))
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
onassis_results <- annotate(geo_chip, 'OBO', dictionary=obo)
entities <- entities(onassis_results)
entities(onassis_results) <- entities[sample(nrow(entities), 30),]
onassis_results <- sim(onassis_results)

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