Load any glyhub dataset

Load any dataset from the shared external data release. Dataset identifiers also name convenience functions that call this loader with the same options.

Usage

glyhub_load(
  dataset,
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Arguments

dataset

Exact dataset identifier from glyhub_catalog(), for example "glyhub_GPST000738_N_B4GalT1" or "glyhub_CPTAC_CCRCC".

kind

"curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.

cache_dir

Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.

refresh

Download the pinned resource again, even if cached.

offline

Prohibit downloads; require a verified local resource.

Value

For kind = "curated", a glyexp::GlycomicSE or glyexp::GlycoproteomicSE. For kind = "raw", an absolute file path.

Details

Downloads and cached files are checked against the package's size and SHA-256 manifest before use. Files are cached by version and hash. Interrupted or invalid downloads never replace a verified cached file. refresh = TRUE cannot be combined with offline = TRUE. Delete downloaded files from cache_dir to clear the cache.

Dataset objects are no longer exposed through LazyData or data(). Use this loader or each dataset's same-named function. Both return identical objects and share the verified cache. Consult dataset help for scientific details.

See also

glyhub_catalog(), glyhub_data_conventions

Examples

glyhub_catalog()[1:3, c("dataset", "bytes")]
#> # A tibble: 3 × 2
#>   dataset                      bytes
#>   <chr>                        <int>
#> 1 glyhub_GPST000738_N_B4GalT1  85324
#> 2 glyhub_GPST000738_N_ST6GAL1  86980
#> 3 glyhub_GPST000643_O         136920