Ensembl2GO {ViSEAGO} | R Documentation

## Check available organisms datasets at Ensembl.

### Description

List Ensembl referenced organisms datasets from the current (NULL) or archive (number in `character`) annotation version.

### Usage

    Ensembl2GO(biomart = "genes", host = "www.ensembl.org", version = NULL)

### Arguments

`biomart` | the biomart name (eg. "genes", the default) available with biomaRt package `listEnsembl`.
`host` | the Ensembl host adress for vertebrate ("www.ensembl.org", the default value), plants ("plants.ensembl.org"), metazoa ("metazoa.ensembl.org"), or fungi ("fungi.ensembl.org").
`version` | the annotation version to use (eg. NULL for the default current version, or a version number in `character`)

### Details

This function gives referenced organisms genomes at Ensembl. It uses the `useEnsembl` and `listDatasets` from biomaRt package.

### Value

a `genomic_ressource-class` object required by `annotate`.

### 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.

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()`, `EntrezGene2GO()`, `Uniprot2GO()`, `annotate()`, `available_organisms()`, `genomic_ressource-class`, `taxonomy()`

### Examples

    # host address to use for Ensembl vertebrate/Plants/Protists/Metazoa/Fungi
    # host="www.ensembl.org" # vertebrate
    # host="plants.ensembl.org"
    # host="protists.ensembl.org"
    # host="metazoa.ensembl.org"
    # host="fungi.ensembl.org"
    # biomart is not available for bacteria

    ## Not run:
    # check the Ensembl available biomart (if not known)
    # for Animals (host="www.ensembl.org", the default)
    biomaRt::listEnsembl()

    # List Ensembl available organisms
    Ensembl<-ViSEAGO::Ensembl2GO(
     biomart="genes",
     host="www.ensembl.org",
     version=NULL
    )

    ## End(Not run)

[Package ViSEAGO version 1.6.0 Index]