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

[Package DAPAR version 1.24.8 Index]