R: 'sim'

sim {Onassis}

R Documentation

`sim`

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)

[Package Onassis version 1.9.3 Index]