Custom2GO: Store organisms GO annotations from custom database file.

In ViSEAGO: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Description

Store the available species and current GO annotations from a custom table file

Usage

Custom2GO(file)

Arguments

file	custom GO annotation file

Details

This function load a custom GO annotation database table that must contain columns:

taxid

custom taxonomic identifiants

gene_id

custom gene identifiants

gene_symbol

custom gene symbols

GOID

Known GO identifiants (see select(GO.db,columns=columns(GO.db),keys=keys(GO.db))

evidence

Known GO evidence codes

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.

See Also

Other genomic_ressource: Bioconductor2GO(), Ensembl2GO(), EntrezGene2GO(), Uniprot2GO(), annotate(), available_organisms(), genomic_ressource-class, taxonomy()

Examples

# Download custom GO annotations
Custom<-ViSEAGO::Custom2GO(
    system.file(
        "extdata/customfile.txt",
        package = "ViSEAGO"
    )
)

Example output

Warning message:
replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ 
'select()' returned 1:1 mapping between keys and columns

ViSEAGO documentation built on Nov. 8, 2020, 6:51 p.m.