cBioCache-deprecated: Deprecated cache helper functions

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

Deprecated cache helper functions

Description

'cBioPortalData' no longer caches data from API responses; therefore, 'removeDataCache' is no longer needed. It will be removed as soon as the next release of Bioconductor.

Usage

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

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')
dry.run	logical Whether or not to remove cache files (default TRUE).
...	Additional arguments to lower level API functions

Value

removeDataCache: The path to the cache location when 'dry.run = FALSE' if the file exists. Otherwise, when 'dry.run = TRUE', the function return the output of the 'file.remove' operation.

removeDataCache

Remove the computed cache location based on the function inputs to 'cBioPortalData()'. To remove the cache, simply replace the 'cBiocPortalData()' function name with 'removeDataCache()'; see the example. If the computed cache location is not found, it will return an empty vector.

Examples

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. 22, 2024, 1:02 a.m.