collapse: 'collapse'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method collapses semantic states in an Onassis object.

Usage

collapse(onassis = NA, simil_thresh)

## S4 method for signature 'Onassis'
collapse(onassis = NA, simil_thresh)

Arguments

onassis	instance of class Onassis-class
simil_thresh	the semantic similarity threshold to use to merge similar semantic sets

Value

a new object of class Onassis-class with collapsed annotations for the entities and a new similarity matrix of similarities between newly created semantic sets

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), 15),]
onassis_results <- sim(onassis_results)
collapsed_onassis <- collapse(onassis_results, 0.9)

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