go_annot_download: Gene annotations from Gene Ontology

In saezlab/OmnipathR: OmniPath web service client and more

Gene annotations from Gene Ontology

Description

Gene Ontology is an ontology of gene subcellular localizations, molecular functions and involvement in biological processes. Gene products across many organisms are annotated with the ontology terms. This function downloads the gene-ontology term associations for certain model organisms or all organisms. For a description of the columns see http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/.

Usage

go_annot_download(organism = "human", aspects = c("C", "F", "P"), slim = NULL)

Arguments

organism	Character: either "chicken", "cow", "dog", "human", "pig" or "uniprot_all".
aspects	Character vector with some of the following elements: "C" (cellular component), "F" (molecular function) and "P" (biological process). Gene Ontology is three separate ontologies called as three aspects. By this parameter you can control which aspects to include in the output.
slim	Character: if not NULL, the name of a GOsubset (slim). instead of the full GO annotation, the slim annotation will be returned. See details at go_annot_slim. If TRUE, the "generic" slim will be used.

Value

A tibble (data frame) of annotations as it is provided by the database

Examples

goa_data <- go_annot_download()
goa_data
# # A tibble: 606,840 x 17
#    db       db_object_id db_object_symbol qualifier go_id   db_ref
#    <fct>    <chr>        <chr>            <fct>     <chr>   <chr>
#  1 UniProt. A0A024RBG1   NUDT4B           NA        GO:000. GO_REF:00.
#  2 UniProt. A0A024RBG1   NUDT4B           NA        GO:000. GO_REF:00.
#  3 UniProt. A0A024RBG1   NUDT4B           NA        GO:004. GO_REF:00.
#  4 UniProt. A0A024RBG1   NUDT4B           NA        GO:005. GO_REF:00.
#  5 UniProt. A0A024RBG1   NUDT4B           NA        GO:005. GO_REF:00.
# # . with 606,830 more rows, and 11 more variables:
# #   evidence_code <fct>, with_or_from <chr>, aspect <fct>,
# #   db_object_name <chr>, db_object_synonym <chr>,
# #   db_object_type <fct>, taxon <fct>, date <date>,
# #   assigned_by <fct>, annotation_extension <chr>,
# #   gene_product_from_id <chr>

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.