Ensembl2GO: Check available organisms datasets at Ensembl.

In abrionne/ViSEAGO: ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

Description

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

Usage

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

Arguments

biomart	the biomart name (eg. "ensembl", 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

###################
# 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="ensembl",
 host="www.ensembl.org",
 version=NULL
)

abrionne/ViSEAGO documentation built on June 13, 2019, 2:27 p.m.