R: Download and process TCGA data

loadTCGAdata {psichomics}

R Documentation

Download and process TCGA data

Description

TCGA data obtained via FireBrowse

Usage

loadTCGAdata(
  folder = getDownloadsFolder(),
  data = c("clinical", "junction_quantification", "RSEM_genes"),
  exclude = c(".aux.", ".mage-tab.", "MANIFEST.txt"),
  ...,
  download = TRUE
)

Arguments

`folder`	Character: directory to store the downloaded archives (by default, saves to `getDownloadsFolder()`)
`data`	Character: data to load (see `getTCGAdataTypes()`)
`exclude`	Character: files and folders to exclude from downloading and from loading into R (by default, exclude files containing `.aux.`, `.mage-tab.` and `MANIFEST.TXT`)
`...`	Arguments passed on to `queryFirebrowseData` `date` Character: dates of the data retrieval by FireBrowse (by default, it uses the most recent data available) `cohort` Character: abbreviation of the cohorts (by default, returns data for all cohorts) `data_type` Character: data types (optional) `tool` Character: data produced by the selected FireBrowse tools (optional) `platform` Character: data generation platforms (optional) `center` Character: data generation centres (optional) `level` Integer: data levels (optional) `protocol` Character: sample characterization protocols (optional) `page` Integer: page of the results to return (optional) `page_size` Integer: number of records per page of results (optional) `sort_by` String: column used to sort the data (by default, sort by cohort)
`download`	Boolean: download missing files

Value

A list with the loaded data, unless required files are unavailable and download = FALSE (if so, it returns the URL of files to download)

Examples

getTCGAcohorts()
getTCGAdataTypes()
## Not run: 
loadTCGAdata(cohort = "ACC", data_type = "Clinical")

## End(Not run)