getTCGAdatalist: Import Terra TCGA data as a list

View source: R/terraTCGAdata.R

getTCGAdatalistR Documentation

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 (AnVIL::gcloud_exists())
  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"
  )


waldronlab/terraTCGAdata documentation built on May 4, 2024, 10:54 p.m.