Retrieve the GO terms associated to a gene

get_gene_go_terms(
  gene,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

gene: An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc
raw: TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised: Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file: The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite: Whether or not to overwrite if a file exists at the specified filename.

Value

A data table with information about the GO terms assigned to the queried gene. A list if raw = TRUE. A 404 error if the given identifier does not map to any object.

The fields of the output data.table are:

term.name: Name of the term
term.ID: ID of the term
term.URI: URI of the term

Examples

get_gene_go_terms(3091)
#>                                                                term.name
#>                                                                   <char>
#>   1:                                       sequence-specific DNA binding
#>   2:                                                body fluid secretion
#>   3: positive regulation of G protein-coupled receptor signaling pathway
#>   4:                    positive regulation of epithelial cell migration
#>   5:                                                 glucose homeostasis
#>  ---                                                                    
#> 618:                                                      tube formation
#> 619:                        cellular response to monosaccharide stimulus
#> 620:                          cellular response to carbohydrate stimulus
#> 621:                              regulation of T cell apoptotic process
#> 622:                     negative regulation of T cell apoptotic process
#>         term.ID                                  term.URI
#>          <char>                                    <char>
#>   1: GO:0043565 http://purl.obolibrary.org/obo/GO_0043565
#>   2: GO:0007589 http://purl.obolibrary.org/obo/GO_0007589
#>   3: GO:0045745 http://purl.obolibrary.org/obo/GO_0045745
#>   4: GO:0010634 http://purl.obolibrary.org/obo/GO_0010634
#>   5: GO:0042593 http://purl.obolibrary.org/obo/GO_0042593
#>  ---                                                     
#> 618: GO:0035148 http://purl.obolibrary.org/obo/GO_0035148
#> 619: GO:0071326 http://purl.obolibrary.org/obo/GO_0071326
#> 620: GO:0071322 http://purl.obolibrary.org/obo/GO_0071322
#> 621: GO:0070232 http://purl.obolibrary.org/obo/GO_0070232
#> 622: GO:0070233 http://purl.obolibrary.org/obo/GO_0070233