terraTCGAworkspace: Obtain or set the Terra Workspace Project Dataset

In waldronlab/terraTCGAdata: OpenAccess TCGA Data on Terra as MultiAssayExperiment

Obtain or set the Terra Workspace Project Dataset

Description

Terra allows access to about 71 open access TCGA datasets. A dataset workspace can be set using the terraTCGAworkspace function with a projectName input. Use the selectTCGAworkspace function to select a TCGA data workspace from an interactive table.

Usage

terraTCGAworkspace(projectName = getOption("terraTCGAdata.workspace", NULL))

selectTCGAworkspace(
  projectName = getOption("terraTCGAdata.workspace", NULL),
  verbose = FALSE,
  ...
)

Arguments

projectName	character(1) A project code usually in the form of ⁠TCGA_CODE_OpenAccess_V1-0_DATA⁠. See selectTCGAworkspace to interactively select from a table of project codes.
verbose	logical(1) Whether to provide more informative messages when an the "terraTCGAdata.workspace" option is set.
...	further arguments passed down to lower level functions, not intended for the end user.

Details

Note that GDC workspaces are not supported and are excluded from the search results. GDC workspaces use a Terra workflow to download TCGA data rather than providing Google Bucket storage locations for easy data retrieval. To reset the terraTCGAworkspace, use terraTCGAworkspace(NULL) and you will be prompted to select from a list of TCGA workspaces. You may also check the current active workspace by running terraTCGAworkspace() without any inputs.

Value

A Terra TCGA Workspace name

Functions

• selectTCGAworkspace(): Function to interactively select from the available TCGA data workspaces in Terra. The 'projectName' argument and 'terraTCGAdata.workspace' option must be 'NULL' to enable the interactive gadget.

Examples

if (
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP") &&
    nzchar(AnVILGCP::avworkspace_name())
) {
  selectTCGAworkspace()
  terraTCGAworkspace()
}

waldronlab/terraTCGAdata documentation built on Nov. 2, 2024, 11:38 a.m.