group_GO: Calculates the GO profile of a vector of genes/proteins at a...

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

Calculates the GO profile of a vector of genes/proteins at a given level of the Gene Ontology

Description

This function is a wrappper to the function groupGO from the package 'clusterProfiler'. Given a vector of genes/proteins, it returns the GO profile at a specific level. It returns a groupGOResult instance.

Usage

group_GO(data, idFrom, orgdb, ont, level, readable = FALSE)

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	on which ontology to perform the analysis (MF, BP or CC)
level	level of the ontolofy to perform the analysis
readable	TRUE or FALSE (default FALSE)

Value

GO profile at a specific level

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)
ggo <- group_GO(
    data = Biobase::fData(obj)$Protein.IDs, idFrom = "UNIPROT",
    orgdb = "org.Sc.sgd.db", ont = "MF", level = 2
)

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