Retrieve the annotations of a dataset

get_dataset_annotations(
  dataset,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

dataset: A numerical dataset identifier or a dataset short name
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 annotations of the queried dataset. 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:

class.name: Name of the annotation class (e.g. organism part)
class.URI: URI for the annotation class
term.name: Name of the annotation term (e.g. lung)
term.URI: URI for the annotation term
object.class: Class of object that the term originated from.

Examples

get_dataset_annotations("GSE2018")
#>       class.name                            class.URI
#>           <char>                               <char>
#> 1:       disease http://www.ebi.ac.uk/efo/EFO_0000408
#> 2: organism part http://www.ebi.ac.uk/efo/EFO_0000635
#> 3:       disease http://www.ebi.ac.uk/efo/EFO_0000408
#>                                         term.name
#>                                            <char>
#> 1:                                          acute
#> 2:                                           lung
#> 3: disease related to solid organ transplantation
#>                                         term.URI  object.class
#>                                           <char>        <char>
#> 1:   http://purl.obolibrary.org/obo/PATO_0000389   FactorValue
#> 2: http://purl.obolibrary.org/obo/UBERON_0002048 ExperimentTag
#> 3:  http://purl.obolibrary.org/obo/MONDO_0700221   FactorValue