go_annot_slim: GO slim gene annotations

In saezlab/OmnipathR: OmniPath web service client and more

GO slim gene annotations

Description

GO slims are subsets of the full GO which "give a broad overview of the ontology content without the detail of the specific fine grained terms". In order to annotate genes with GO slim terms, we take the annotations and search all ancestors of the terms up to the root of the ontology tree. From the ancestors we select the terms which are part of the slim subset.

Usage

go_annot_slim(
  organism = "human",
  slim = "generic",
  aspects = c("C", "F", "P"),
  cache = TRUE
)

Arguments

organism	Character: either "chicken", "cow", "dog", "human", "pig" or "uniprot_all".
slim	Character: the GO subset (GO slim) name. Available GO slims are: "agr" (Alliance for Genomics Resources), "generic", "aspergillus", "candida", "drosophila", "chembl", "metagenomic", "mouse", "plant", "pir" (Protein Information Resource), "pombe" and "yeast".
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.
cache	Logical: Load the result from cache if available.

Details

Building the GO slim is resource intensive in its current implementation. For human annotation and generic GO slim it might take around 20 minutes. The result is saved into the cache so next time loading the data from there is really quick. If the cache option is FALSE the data will be built fresh (the annotation and ontology files still might come from cache), and the newly build GO slim will overwrite the cache instance.

Value

A tibble (data frame) of genes annotated with ontology terms in in the GO slim (subset).

See Also

• go_annot_download

• go_ontology_download

• get_db

Examples

## Not run: 
goslim <- go_annot_slim(organism = 'human', slim = 'generic')
goslim
# # A tibble: 276,371 x 8
#    db     db_object_id db_object_symbol go_id aspect db_object_name
#    <fct>  <chr>        <chr>            <chr> <fct>  <chr>
#  1 UniPr. A0A024RBG1   NUDT4B           GO:0. F      Diphosphoinosito.
#  2 UniPr. A0A024RBG1   NUDT4B           GO:0. F      Diphosphoinosito.
#  3 UniPr. A0A024RBG1   NUDT4B           GO:0. C      Diphosphoinosito.
#  4 UniPr. A0A024RBG1   NUDT4B           GO:0. C      Diphosphoinosito.
#  5 UniPr. A0A024RBG1   NUDT4B           GO:0. C      Diphosphoinosito.
# # . with 276,366 more rows, and 2 more variables:
# #   db_object_synonym <chr>, db_object_type <fct>

## End(Not run)

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.