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 1.4.5 Index]