getClinicalTable: Obtain the reference table for clinical data

In LiNk-NY/terraTCGAdata: OpenAccess TCGA Data on Terra as MultiAssayExperiment

Obtain the reference table for clinical data

Description

The column names in the output table can be used in the getClinical function.

Usage

getClinicalTable(
  tablename = .DEFAULT_TABLENAME,
  metacols = .PARTICIPANT_METADATA_COLS,
  workspace = terraTCGAworkspace(),
  namespace = .DEFAULT_NAMESPACE,
  verbose = TRUE
)

Arguments

tablename	The Terra data model table from which to extract the clinical data (default: "sample")
metacols	The set of columns that comprise of the metadata columns. See the .PARTICIPANT_METADATA_COLS global variable
workspace	character(1) The Terra Data Resources workspace from which to pull TCGA data (default: see terraTCGAworkspace()). This is set to a package-wide option.
namespace	character(1) The Terra Workspace Namespace that defaults to "broad-firecloud-tcga" and rarely needs to be changed.
verbose	logical(1) Whether to output additional information regarding the workspace and namespace (default: TRUE).

Value

A tibble of Google Storage resource locations e.g., ⁠gs://firecloud...⁠

Examples

if (
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP") &&
    nzchar(AnVILGCP::avworkspace_name())
)
    getClinicalTable(
        workspace = "TCGA_ACC_OpenAccess_V1-0_DATA"
    )

LiNk-NY/terraTCGAdata documentation built on Nov. 4, 2024, 2:07 p.m.