EntrezGene2GO: Store available organisms GO annotations at EntrezGene.

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

Description

Store the available species and current GO annotations from the gene2go.gz nfile avalable at NCBI EntrezGene ftp.

Usage

EntrezGene2GO()

Details

This function downloads the gene2go.gz file from EntrezGene ftp which contains available organisms (taxid) with the corresponding GO annotations.

Value

a genomic_ressource-class object required by annotate.

References

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.

Eric Sayers (2013). Entrez Programming Utilities Help.

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

Maglott, D, Ostell, J, Pruitt, KD, Tatusova, T (2011). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, Database issue:D52-7.

See Also

Other genomic_ressource: Bioconductor2GO, Custom2GO, Ensembl2GO, Uniprot2GO, annotate, available_organisms, genomic_ressource-class, taxonomy

Examples

## Not run: 
###################
# Download EntrezGene available organisms GO annotations
EntrezGene<-ViSEAGO::EntrezGene2GO()

## End(Not run)

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