Manage cache / download directories for study data

Managing data downloads is important to save disk space and avoid re-downloading data files. This can be done via the integrated BiocFileCache system.

Usage

cBioCache(..., ask = interactive())

setCache(
  directory = tools::R_user_dir("cBioPortalData", "cache"),
  verbose = TRUE,
  ask = interactive()
)

removePackCache(cancer_study_id, dry.run = TRUE)

Arguments

...

For cBioCache, arguments passed to setCache

ask

logical (default TRUE when interactive session) Confirm the file location of the cache directory

directory

The file location where the cache is located. Once set future downloads will go to this folder.

verbose

Whether to print descriptive messages

cancer_study_id

character(1) The studyId from getStudies

dry.run

logical Whether or not to remove cache files (default TRUE).

Value

cBioCache: The path to the cache location

cBioCache

Get the directory location of the cache. It will prompt the user to create a cache if not already created. A specific directory can be used via setCache.

setCache

Specify the directory location of the data cache. By default, it will go to the user directory as given by:

tools::R_user_dir("cBioPortalData", "cache")

removePackCache

Some files may become corrupt when downloading, this function allows the user to delete the tarball associated with a cancer_study_id in the cache. This only works for the cBioDataPack function. To remove the entire cBioPortalData cache, run unlink("~/.cache/cBioPortalData").

Examples

cBioCache()
#> [1] "/github/home/.cache/R/cBioPortalData"

removePackCache("acc_tcga", dry.run = TRUE)
#> # A tibble: 1 × 10
#>   rid   rname create_time access_time rpath rtype fpath last_modified_time etag 
#>   <chr> <chr> <chr>       <chr>       <chr> <chr> <chr> <chr>              <chr>
#> 1 BFC4  acc_… 2025-04-22… 2025-04-22… /git… web   http… 2024-12-26 20:18:… e27e…
#> # ℹ 1 more variable: expires <dbl>