annotate {ViSEAGO} | R Documentation

## Retrieve GO annotations for a specie from genomic ressource database.

### Description

This method retrieves and stores GO annotations for the organism of interest from one of genomic ressource database (Bioconductor, EntrezGene, Ensembl, Uniprot).

### Usage

    annotate(id, object, ortholog = FALSE)

    ## S4 method for signature 'character,genomic_ressource'
    annotate(id, object, ortholog = FALSE)

### Arguments

`id` | identifiant corresponding to the organism of interest. This id name is referenced in the first column of the database used (see `available_organisms`).
`object` | a required `genomic_ressource-class` object created by `Bioconductor2GO`, `EntrezGene2GO`, `Ensembl2GO`, or `Uniprot2GO` methods.
`ortholog` | `logical` (default to FALSE). Only available for vertebrates organisms and for object created by `EntrezGene2GO` method (see Details).

### Details

This method uses a `genomic_ressource-class` object to retrieve GO annotations for the organism of interest. The stored annotations are structured in 3 slots corresponding to the 3 GO categories: MF (Molecular Function), BP (Biological Process), and CC (Cellular Component). Each slot contains GO terms with associated evidence code.

The `genomic_ressource-class` object is created by one of the four available methods: `Bioconductor2GO`, `EntrezGene2GO`, `Ensembl2GO`, or `Uniprot2GO`.

In the case of vertebrates, setting `ortholog` argument to `TRUE` is required if you need to add GO terms with experimental evidence codes from orthologs genes when using `EntrezGene2GO` method. To display organisms supported by NCBI EntrezGene orthologs pipeline, set the arguments `id=NULL` and `ortholog=TRUE`. This approch is highly similar to the strategy developed by Uniprot-GOA consortium for the Electronic Annotation Method using Ensembl Compara.

### Value

`annotate` produces an object of `gene2GO-class` required by `build_GO_SS` method.

### References

Durinck S, Spellman P, Birney E and Huber W (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols, 4, pp. 1184-1191.

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A and Huber W (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics, 21, pp. 3439-3440.

Fong, JH, Murphy, TD, Pruitt, KD (2013). Comparison of RefSeq protein-coding regions in human and vertebrate genomes. BMC Genomics, 14:654.

Henrik Bengtsson (2016). R.utils: Various Programming Utilities. R package version 2.5.0. https://CRAN.R-project.org/package=R.utils.

Herve Pages, Marc Carlson, Seth Falcon and Nianhua Li (2017). AnnotationDbi: Annotation Database Interface. R package version 1.38.0.

Matt Dowle and Arun Srinivasan (2017). data.table: Extension of data.frame. R package version 1.10.4. https://CRAN.R-project.org/package=data.table.

### See Also

Other genomic_ressource: `Bioconductor2GO()`, `Custom2GO()`, `Ensembl2GO()`, `EntrezGene2GO()`, `Uniprot2GO()`, `available_organisms()`, `genomic_ressource-class`, `taxonomy()`

Other GO_terms: `GOcount()`, `GOterms_heatmap()`, `create_topGOdata()`, `gene2GO-class`, `merge_enrich_terms()`, `runfgsea()`

### Examples

    ## Not run:
    ## load Mus musculus (mouse) GO annotations

    # from Bioconductor
    Bioconductor<-ViSEAGO::Bioconductor2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="org.Mm.eg.db",
        object=Bioconductor
    )

    # from EntrezGene
    EntrezGene<-ViSEAGO::EntrezGene2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="10090",
        object=EntrezGene
    )

    # from EntrezGene
    Ensembl<-ViSEAGO::Ensembl2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="mmusculus_gene_ensembl",
        object=Ensembl
    )

    # from Uniprot
    Uniprot<-ViSEAGO::Uniprot2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="mouse",
        object=Uniprot
    )

    ## from Custom GO annotation file
    Custom<-ViSEAGO::Custom2GO(system.file("extdata/customfile.txt",package = "ViSEAGO"))
    myGENE2GO<-ViSEAGO::annotate(
        id="myspecies1",
        object=Custom
    )

    ## specific options for EntrezGene database

    # Chicken GO annotations without adding orthologs
    EntrezGene<-ViSEAGO::EntrezGene2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="9031",
        object=EntrezGene
    )

    # Chicken GO annotation with the add of orthologs GO annotations
    EntrezGene<-ViSEAGO::EntrezGene2GO()
    myGENE2GO<-ViSEAGO::annotate(
        id="9031",
        object=EntrezGene,
        ortholog=TRUE
    )

    # display organisms supported by NCBI EntrezGene orthologs pipeline
    EntrezGene<-ViSEAGO::EntrezGene2GO()
    ViSEAGO::annotate(
        id="NULL",
        object=EntrezGene,
        ortholog=TRUE
    )

    ## End(Not run)

[Package ViSEAGO version 1.4.0 Index]