getTopGO: Get the topGO Object function
In klarakaleb/roma: R wrapper for the OMA REST API

getTopGO

R Documentation

Get the topGO Object function

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')

klarakaleb/roma documentation built on Jan. 27, 2024, 3:46 p.m.