getTopGO: Get the topGO Object function

Description Usage Arguments Value Examples

View source: R/getTopGO.R

Description

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

Usage

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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

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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 Nov. 11, 2020, 5:36 a.m.