annotate-methods: Retrieve GO annotations for a specie from genomic ressource...

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

Description

This method retrieves and stores GO annotations for the organism of interest from one of genomic ressource database (Bioconductor, EntrezGene, Ensembl, Uniprot).

Usage

annotate(id, object, ortholog = FALSE)

## S4 method for signature 'character,genomic_ressource'
annotate(id, object,
  ortholog = FALSE)

Arguments

id	identifiant corresponding to the organism of interest. This id name is referenced in the first column of the database used (see available_organisms).
object	a required genomic_ressource-class object created by Bioconductor2GO, EntrezGene2GO, Ensembl2GO, or Uniprot2GO methods.
ortholog	logical (default to FALSE). Only available for vertebrates organisms and for object created by EntrezGene2GO method (see Details).

Details

This method uses a genomic_ressource-class object to retrieve GO annotations for the organism of interest. The stored annotations are structured in 3 slots corresponding to the 3 GO categories: MF (Molecular Function), BP (Biological Process), and CC (Cellular Component). Each slot contains GO terms with associated evidence code.

The genomic_ressource-class object is created by one of the four available methods: Bioconductor2GO, EntrezGene2GO, Ensembl2GO, or Uniprot2GO.

In the case of vertebrates, setting ortholog argument to TRUE is required if you need to add GO terms with experimental evidence codes from orthologs genes when using EntrezGene2GO method. To display organisms supported by NCBI EntrezGene orthologs pipeline, set the arguments id=NULL and ortholog=TRUE. This approch is highly similar to the strategy developed by Uniprot-GOA consortium for the Electronic Annotation Method using Ensembl Compara.

Value

annotate produces an object of gene2GO-class required by build_GO_SS method.

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.

Fong, JH, Murphy, TD, Pruitt, KD (2013). Comparison of RefSeq protein-coding regions in human and vertebrate genomes. BMC Genomics, 14:654.

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

Herve Pages, Marc Carlson, Seth Falcon and Nianhua Li (2017). AnnotationDbi: Annotation Database Interface. R package version 1.38.0.

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, Ensembl2GO, EntrezGene2GO, Uniprot2GO, available_organisms, genomic_ressource-class, taxonomy

Other GO_terms: GOcount, GOterms_heatmap, create_topGOdata, gene2GO-class, merge_enrich_terms

Examples

## Not run: 
## load Mus musculus (mouse) GO annotations

# from Bioconductor
Bioconductor<-ViSEAGO::Bioconductor2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="org.Mm.eg.db",
    object=Bioconductor
)

# from EntrezGene
EntrezGene<-ViSEAGO::EntrezGene2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="10090",
    object=EntrezGene
)

# from EntrezGene
Ensembl<-ViSEAGO::Ensembl2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="mmusculus_gene_ensembl",
    object=Ensembl
)

# from Uniprot
Uniprot<-ViSEAGO::Uniprot2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="mouse",
    object=Uniprot
)

## from Custom GO annotation file
Custom<-ViSEAGO::Custom2GO(system.file("extdata/customfile.txt",package = "ViSEAGO"))
myGENE2GO<-ViSEAGO::annotate(
    id="myspecies1",
    object=Custom
)

## specific options for EntrezGene database

# Chicken GO annotations without adding orthologs
EntrezGene<-ViSEAGO::EntrezGene2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="9031",
    object=EntrezGene
)

# Chicken GO annotation with the add of orthologs GO annotations
EntrezGene<-ViSEAGO::EntrezGene2GO()
myGENE2GO<-ViSEAGO::annotate(
    id="9031",
    object=EntrezGene,
    ortholog=TRUE
)

# display organisms supported by NCBI EntrezGene orthologs pipeline
EntrezGene<-ViSEAGO::EntrezGene2GO()
ViSEAGO::annotate(
    id=NULL,
    object=EntrezGene,
    ortholog=TRUE
)

## End(Not run)

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