getAssayTable: Obtain a reference table for assay data in the Terra data...

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

Obtain a reference table for assay data in the Terra data model

Description

The column names in the output can be used in the getAssayData function.

Usage

getAssayTable(
  tablename = .DEFAULT_TABLENAME,
  metacols = .PARTICIPANT_METADATA_COLS,
  workspace = terraTCGAworkspace(),
  namespace = .DEFAULT_NAMESPACE
)

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.

Value

A tibble of pointers to resources within the Terra data model

Examples

if (
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP") &&
    nzchar(AnVILGCP::avworkspace_name())
)
  getAssayTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA")

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