Ensembl2GO.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Ensembl2GO.R
\name{Ensembl2GO}
\alias{Ensembl2GO}
\title{Check available organisms datasets at Ensembl.}
\usage{
Ensembl2GO(biomart = "genes", host = "www.ensembl.org", version = NULL)
}
\arguments{
\item{biomart}{the biomart name (eg. "genes", the default) available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}}.}

\item{host}{the Ensembl host adress for \href{http://www.ensembl.org/index.html}{vertebrate} ("www.ensembl.org", the default value),
\href{http://www.plants.ensembl.org/index.html}{plants} ("plants.ensembl.org"),
\href{http://www.metazoa.ensembl.org/index.html}{metazoa} ("metazoa.ensembl.org"),
 or \href{http://www.fungi.ensembl.org/index.html}{fungi} ("fungi.ensembl.org").}

\item{version}{the annotation version to use (eg. NULL for the default current version, or a version number in \code{character})}
}
\value{
a  \code{\link{genomic_ressource-class}} object required by \code{\link{annotate}}.
}
\description{
List Ensembl referenced organisms datasets from the current (NULL) or archive (number in \code{character}) annotation version.
}
\details{
This function gives referenced organisms genomes at \href{http://ensemblgenomes.org/}{Ensembl}.
It uses the \code{\link[biomaRt]{useEnsembl}} and  \code{\link[biomaRt]{listDatasets}} from \pkg{biomaRt} package.
}
\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

\dontrun{
# 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
)
}
}
\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.
}
\seealso{
Other genomic_ressource: 
\code{\link{Bioconductor2GO}()},
\code{\link{Custom2GO}()},
\code{\link{EntrezGene2GO}()},
\code{\link{Uniprot2GO}()},
\code{\link{annotate}()},
\code{\link{available_organisms}()},
\code{\link{genomic_ressource-class}},
\code{\link{taxonomy}()}
}
\concept{genomic_ressource}