Ensembl2GO {ViSEAGO} | R Documentation |
List Ensembl referenced organisms datasets from the current (NULL) or archive (number in character
) annotation version.
Ensembl2GO(biomart = "genes", host = "www.ensembl.org", version = NULL)
biomart |
the biomart name (eg. "genes", the default) available with biomaRt package |
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 |
This function gives referenced organisms genomes at Ensembl.
It uses the useEnsembl
and listDatasets
from biomaRt package.
a genomic_ressource-class
object required by annotate
.
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.
Other genomic_ressource:
Bioconductor2GO()
,
Custom2GO()
,
EntrezGene2GO()
,
Uniprot2GO()
,
annotate()
,
available_organisms()
,
genomic_ressource-class
,
taxonomy()
# 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)