filterconcepts: 'filterconcepts'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method filters unwanted concepts from the entities of an Onassis-class object

Usage

filterconcepts(onassis, concepts_to_filter)

## S4 method for signature 'Onassis'
filterconcepts(onassis, concepts_to_filter = c())

Arguments

onassis	An object of class Onassis-class with already annotated entities
concepts_to_filter	A vector with unwanted concepts

Value

the instance of Onassis-class with filtered entities

Examples

geo_chip <- readRDS(system.file('extdata', 'vignette_data',
'GEO_human_chip.rds', package='Onassis'))
geo_chip <- geo_chip[sample(nrow(geo_chip), 15) ,]
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
onassis_results <- annotate(geo_chip, 'OBO', dictionary=obo)
filtered_onassis <- filterconcepts(onassis_results, c('cell'))

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