downloadStudy: Manually download, untar, and load study tarballs

In cBioPortalData: Exposes and makes available data from the cBioPortal web resources

Description

Note that these functions should be used when a particular study is not currently available as a MultiAssayExperiment representation. Otherwise, use cBioDataPack. Provide a cancer_study_id from the studiesTable and retrieve the study tarball from cBioPortal. These functions are used by cBioDataPack under the hood to download, untar, and load the tarball datasets with caching. As stated in ?cBioDataPack, not all studies are currently working as MultiAssayExperiment objects. As of July 2020, about ~80% of datasets can be successfully imported into the MultiAssayExperiment data class. Please open an issue if you would like the team to prioritize a study. You may also check studiesTable$pack_build for a more current status.

Usage

downloadStudy(
  cancer_study_id,
  use_cache = TRUE,
  force = FALSE,
  url_location = getOption("cBio_URL", .url_location)
)

untarStudy(cancer_study_file, exdir = tempdir())

loadStudy(filepath, names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene"))

Arguments

cancer_study_id	character(1) The study identifier from cBioPortal as in https://cbioportal.org/webAPI
use_cache	logical(1) (default TRUE) create the default cache location and use it to track downloaded data. If data found in the cache, data will not be re-downloaded. A path can also be provided to data cache location.
force	logical(1) (default FALSE) whether to force re-download data from remote location
url_location	character(1) (default "https://cbioportal-datahub.s3.amazonaws.com") the URL location for downloading packaged data. Can be set using the 'cBio_URL' option (see ?cBioDataPack for more details)
cancer_study_file	character(1) indicates the on-disk location of the downloaded tarball
exdir	character(1) indicates the folder location to put the contents of the tarball (default tempdir(); see also ?untar)
filepath	character(1) indicates the folder location where the contents of the tarball are located (usually the same as exdir)
names.field	A character vector of possible column names for the column that is used to label ranges from a mutations or copy number file.

Value

• downloadStudy - The file location of the data tarball

• untarStudy - The directory location of the contents

• loadStudy - A MultiAssayExperiment-class object

See Also

cBioDataPack, MultiAssayExperiment

Examples

(acc_file <- downloadStudy("acc_tcga"))

(file_dir <- untarStudy(acc_file, tempdir()))

loadStudy(file_dir)

cBioPortalData documentation built on April 17, 2021, 6:07 p.m.