enrich_GO: Calculates GO enrichment classes for a given list of...

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(10)]
if (!requireNamespace("org.Sc.sgd.db", quietly = TRUE)) {
stop("Please install org.Sc.sgd.db: 
            BiocManager::install('org.Sc.sgd.db')")
}
library(org.Sc.sgd.db)
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
)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.