enrich_GO {DAPAR}R Documentation

Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.

Description

This function is a wrappper to the function enrichGO from the package clusterProfiler. Given a vector of genes/proteins, it returns an enrichResult instance.

Usage

enrich_GO(data, idFrom, orgdb, ont, readable = FALSE, pval, universe)

Arguments

data

A vector of ID (among ENSEMBL, ENTREZID, GENENAME, REFSEQ, UNIGENE, UNIPROT -can be different according to organisms)

idFrom

character indicating the input ID format (among ENSEMBL, ENTREZID, GENENAME, REFSEQ, UNIGENE, UNIPROT)

orgdb

annotation Bioconductor package to use (character format)

ont

One of "MF", "BP", and "CC" subontologies

readable

TRUE or FALSE (default FALSE)

pval

The qvalue cutoff (same parameter as in the function enrichGO of the package clusterProfiler)

universe

a list of ID to be considered as the background for enrichment calculation

Value

A groupGOResult instance.

Author(s)

Florence Combes

Examples


utils::data(Exp1_R25_prot, package='DAPARdata')
univ<-univ_AnnotDbPkg("org.Sc.sgd.db") #univ is the background
ego<-enrich_GO(data=fData(Exp1_R25_prot)$Protein.IDs, idFrom="UNIPROT", 
orgdb="org.Sc.sgd.db",ont="MF", pval=0.05, universe = univ)


[Package DAPAR version 1.18.5 Index]