cBioCache: Manage cache / download directories for study data

In waldronlab/MultiAssayExperimentData: Exposes and Makes Available Data from the cBioPortal Web Resources

Manage cache / download directories for study data

Description

Managing data downloads is important to save disk space and re-downloading data files. This can be done effortlessly 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)

removeDataCache(
  api,
  studyId = NA_character_,
  genePanelId = NA_character_,
  genes = NA_character_,
  molecularProfileIds = NULL,
  sampleListId = NULL,
  sampleIds = NULL,
  by = c("entrezGeneId", "hugoGeneSymbol"),
  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).
api	An API object of class 'cBioPortal' from the 'cBioPortal' function
studyId	character(1) Indicates the "studyId" as taken from 'getStudies'
genePanelId	character(1) Identifies the gene panel, as obtained from the 'genePanels' function
genes	character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses.
molecularProfileIds	character() A vector of molecular profile IDs
sampleListId	character(1) A sample list identifier as obtained from 'sampleLists()“
sampleIds	character() Sample identifiers
by	character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId')

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()

removePackCache("acc_tcga", dry.run = TRUE)


cbio <- cBioPortal()

cBioPortalData(
    cbio, by = "hugoGeneSymbol",
    studyId = "acc_tcga",
    genePanelId = "AmpliSeq",
    molecularProfileIds =
        c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations")
)

removeDataCache(
    cbio, by = "hugoGeneSymbol",
    studyId = "acc_tcga",
    genePanelId = "AmpliSeq",
    molecularProfileIds =
        c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations"),
    dry.run = TRUE
)

waldronlab/MultiAssayExperimentData documentation built on Nov. 2, 2024, 3:19 a.m.