Skip to contents

GO slim gene annotations

Source: R/go.R
go_annot_slim.Rd

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.

Value

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

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.

See also

Examples

if (FALSE) {
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>
}