getTCGAdatalist: Import Terra TCGA data as a list

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

Import Terra TCGA data as a list

Description

Import Terra TCGA data as a list

Usage

getTCGAdatalist(
  assayNames,
  sampleCode,
  workspace = terraTCGAworkspace(),
  namespace = .DEFAULT_NAMESPACE,
  tablename = .DEFAULT_TABLENAME,
  sampleIdx = TRUE,
  verbose = TRUE
)

Arguments

assayNames	character() A vector of assays selected from the colnames of getAssayTable.
sampleCode	character(1) The sample code used to filtering samples e.g., "01" for Primary Solid Tumors, see data("sampleTypes", package = "TCGAutils") for reference
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")
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)
verbose	logical(1L) Whether to output additional details of the data facilitation.

Value

A list of assay datasets

Examples

if (
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP") &&
    nzchar(AnVILGCP::avworkspace_name())
)
  getTCGAdatalist(
      assayNames = c("protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
      "snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg"),
      sampleCode = c("01", "10"),
      workspace = "TCGA_COAD_OpenAccess_V1-0_DATA"
  )

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