## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, cache = TRUE) ## ----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=AnVIL::gcloud_exists()---------------------------------------------- # gcloud_project() ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # selectTCGAworkspace() ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # terraTCGAworkspace("TCGA_COAD_OpenAccess_V1-0_DATA") # getOption("terraTCGAdata.workspace") ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # ct <- getClinicalTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA") # ct # names(ct) ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # 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=AnVIL::gcloud_exists()---------------------------------------------- # at <- getAssayTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA") # at # names(at) ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # sampleTypesTable(workspace = "TCGA_COAD_OpenAccess_V1-0_DATA") ## ----eval=AnVIL::gcloud_exists()---------------------------------------------- # 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=AnVIL::gcloud_exists()---------------------------------------------- # 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()