## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
isAnVILWS <- function() {
    AnVILGCP::gcloud_exists() &&
    identical(AnVILBase::avplatform_namespace(), "AnVILGCP")
}

## ----eval=FALSE---------------------------------------------------------------
#  if (!require("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("terraTCGAdata")

## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------
library(AnVIL)
library(terraTCGAdata)

## -----------------------------------------------------------------------------
gcloud_exists()

## ----eval=isAnVILWS()---------------------------------------------------------
#  gcloud_project()

## ----eval=isAnVILWS()---------------------------------------------------------
#  selectTCGAworkspace()

## ----eval=isAnVILWS()---------------------------------------------------------
#  terraTCGAworkspace("TCGA_COAD_OpenAccess_V1-0_DATA")
#  getOption("terraTCGAdata.workspace")

## ----eval=isAnVILWS()---------------------------------------------------------
#  ct <- getClinicalTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA")
#  ct
#  names(ct)

## ----eval=isAnVILWS()---------------------------------------------------------
#  column_name <- "clin__bio__nationwidechildrens_org__Level_1__biospecimen__clin"
#  clin <- getClinical(
#      columnName = column_name,
#      participants = TRUE,
#      workspace = "TCGA_COAD_OpenAccess_V1-0_DATA"
#  )
#  clin[, 1:6]
#  dim(clin)

## ----eval=isAnVILWS()---------------------------------------------------------
#  at <- getAssayTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA")
#  at
#  names(at)

## ----eval=isAnVILWS()---------------------------------------------------------
#  sampleTypesTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA")

## ----eval=isAnVILWS()---------------------------------------------------------
#  prot <- getAssayData(
#      assayName = "protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
#      sampleCode = c("01", "10"),
#      workspace = "TCGA_COAD_OpenAccess_V1-0_DATA",
#      sampleIdx = 1:4
#  )
#  head(prot)

## ----eval=isAnVILWS()---------------------------------------------------------
#  mae <- terraTCGAdata(
#      clinicalName = "clin__bio__nationwidechildrens_org__Level_1__biospecimen__clin",
#      assays =
#          c("protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
#          "rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data"),
#      sampleCode = NULL,
#      split = FALSE,
#      sampleIdx = 1:4,
#      workspace = "TCGA_COAD_OpenAccess_V1-0_DATA"
#  )
#  mae

## -----------------------------------------------------------------------------
sessionInfo()