Retrieve all publications associated with a dataset

get_dataset_publications(
  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 containing references. The fields of the output data.table are:

title: Title of the paper
authors: List of authors
citation: Citation string for the paper
pmid: PMID of the paper
url: Pubmed URL of the paper

Examples

get_dataset_publications(1)
#>                                                                                 title
#>                                                                                <char>
#> 1: Gene expression profiling of bronchoalveolar lavage cells in acute lung rejection.
#>                                                                                      authors
#>                                                                                       <char>
#> 1: Gimino, Vincent J; Lande, Jeffrey D; Berryman, Todd R; King, Richard A; Hertz, Marshall I
#>                                                                                                                                                       citation
#>                                                                                                                                                         <char>
#> 1: Gimino, Vincent J et al. (2003) Gene expression profiling of bronchoalveolar lavage cells in acute lung rejection.; Am J Respir Crit Care Med, 168: 1237-42
#>        pmid                                          url
#>      <char>                                       <char>
#> 1: 12958056 https://www.ncbi.nlm.nih.gov/pubmed/12958056