sampleTypesTable: Get an overview of the samples available in the workspace

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

Get an overview of the samples available in the workspace

Description

The function provides an overview of samples from the avtables("sample") table for the current workspace. Along with the sample codes and frequencies, the output provides a description for each code and the short letter codes.

Usage

sampleTypesTable(
  workspace = terraTCGAworkspace(),
  namespace = .DEFAULT_NAMESPACE,
  tablename = .DEFAULT_TABLENAME,
  verbose = TRUE
)

Arguments

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.
tablename	The Terra data model table from which to extract the clinical data (default: "sample")
verbose	logical(1) Whether to output additional information regarding the workspace and namespace (default: TRUE).

Value

A tibble of sample codes and frequency along with their definition and short letter code

Examples

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

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