Retrieve the design of a dataset

Retrieve the design of a dataset

get_dataset_design(
  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 of the design matrix for the queried dataset. A 404 error if the given identifier does not map to any object

Examples

head(gemma.R:::get_dataset_design("GSE2018"))
#> Error in data.frame(m, row.names = stringr::str_extract(m$Bioassay, "(?<=Name=).*")): row names contain missing values