getTopGO: Get the topGO Object function

In OmaDB: R wrapper for the OMA REST API

Description

The function to create a topGO object containing the GO annotations for the given protein list.

Usage

getTopGO(annotations, format, foregroundGenes, ontology)

Arguments

annotations	list of GO annoatations obtained from the formatTopGO()
format	Format for the data to be returned in - either 'GO2geneID' or 'geneID2GO'
foregroundGenes	List of identifiers for the foreground genes
ontology	The ontology for which the enrichment should be done. This parameter is passed directly to the topGOdata constructor.

Value

topGO object

Examples

geneList = list(getProtein(id='YEAST58'),getProtein(id='YEAST00059'))
annotations = formatTopGO(geneList,format='geneID2GO')
library(topGO)
getTopGO(annotations, foregroundGenes = list('YEAST00058'), format = 'geneID2GO', ontology = 'BP')

OmaDB documentation built on Nov. 13, 2020, 2 a.m.