getAssayData: Obtain assay datasets from Terra

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

Obtain assay datasets from Terra

Description

Obtain assay datasets from Terra

Usage

getAssayData(
  assayName,
  sampleCode = "01",
  tablename = .DEFAULT_TABLENAME,
  workspace = terraTCGAworkspace(),
  namespace = .DEFAULT_NAMESPACE,
  metacols = .PARTICIPANT_METADATA_COLS,
  sampleIdx = TRUE
)

Arguments

assayName	character() The name of the assay dataset column from getAssayTable to import into the current workspace.
sampleCode	character(1) The sample code used to filtering samples e.g., "01" for Primary Solid Tumors, see data("sampleTypes", package = "TCGAutils") for reference
tablename	The Terra data model table from which to extract the clinical data (default: "sample")
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.
metacols	The set of columns that comprise of the metadata columns. See the .PARTICIPANT_METADATA_COLS global variable
sampleIdx	numeric() index or TRUE. Specify an index for subsetting the assay data. This argument is mainly used for example and vignette purposes. To use all the data, use the default value (default: TRUE)

Value

Either a matrix or RaggedExperiment depending on the assay selected

See Also

getAssayTable()

Examples

if (
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP") &&
    nzchar(AnVILGCP::avworkspace_name())
)
  getAssayData(
      assayName = "protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
      sampleCode = c("01", "10"),
      workspace = "TCGA_ACC_OpenAccess_V1-0_DATA"
  )

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